diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index d5e0f8a6..0e012c9e 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -53,8 +53,6 @@ jobs: gauntlet: runs-on: ubuntu-22.04 - env: - CACHE_DIR: ~/.config/wdl-grammar steps: - uses: actions/checkout@v3 - name: Update Rust diff --git a/Gauntlet.toml b/Gauntlet.toml index 240b17c4..50776ba6 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -36495,6 +36495,11 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] line contains only whitespace (113:1-113:4)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (128:1-128:4)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -36510,6 +36515,11 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] line contains only whitespace (233:1-233:6)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (234:1-234:6)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -36525,11 +36535,41 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] line contains only whitespace (242:1-242:6)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (243:1-243:6)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] line contains only whitespace (247:1-247:4)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (248:1-248:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (251:1-251:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (254:1-254:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (257:1-257:6)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (262:1-262:4)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -36540,31 +36580,66 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] trailing space (111:21)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] trailing space (115:82)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] trailing space (119:40)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] trailing space (126:21)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] trailing space (134:40)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] trailing space (30:180)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] trailing space (33:180)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W001::Style/Low] trailing space (47:73)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W001::Style/Low] trailing space (56:73)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (189:9-189:50)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpuPlatform (204:9-204:50)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nthreads (188:9-188:25)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nthreads (203:9-203:25)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -36580,6 +36655,31 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (129:6-129:14)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (138:14-138:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:14-140:20)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:6-144:14)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (16:12-16:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:12-17:19)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -36595,11 +36695,36 @@ kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (189:16-189:27)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:12-18:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:6-199:19)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (201:14-201:23)" + +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (204:16-204:27)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (266:12-266:26)" +[[concerns]] +kind = "LintWarning" +document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (281:12-281:26)" + [[concerns]] kind = "LintWarning" document = "broadinstitute/warp:tasks/skylab/PairedTagUtils.wdl" @@ -48920,11 +49045,6 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (27:6-27:16)" -[[concerns]] -kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/diamond/diamond.wdl" -message = "[v1::W007::Spacing/Low] missing newline at the end of the file (48:2-48:2)" - [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/host-genome-generation/run.wdl" @@ -49070,21 +49190,61 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:29)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:14-193:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:14-194:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:14-195:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:14-196:34)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (196:19-196:34)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:20-200:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (213:14-213:32)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (216:14-216:32)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (217:6-217:22)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (224:6-224:18)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (243:6-243:15)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -49095,11 +49255,61 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (263:6-263:26)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (267:6-267:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:16-26:48)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (271:21-271:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (27:16-27:49)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (284:6-284:27)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (286:14-286:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (28:16-28:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (295:6-295:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (29:16-29:45)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (312:6-312:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (329:6-329:26)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" @@ -49110,26 +49320,91 @@ kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (350:17-350:23)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (367:6-367:27)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (429:6-429:27)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (430:6-430:27)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (434:16-434:17)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (435:16-435:17)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (459:19-459:33)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (460:19-460:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (469:6-469:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (473:21-473:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:20-49:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (523:6-523:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:10-63:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:10-64:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (65:10-65:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (66:10-66:39)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (95:14-95:32)" +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/index-generation/index-generation.wdl" +message = "[v1::W007::Spacing/Low] missing newline at the end of the file (551:2-551:2)" + [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/legacy-host-filter/legacy-host-filter.wdl" @@ -49923,5507 +50198,7902 @@ message = "[v1::W003::Completeness/Medium] missing parameter meta within task: a [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (691:9-691:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (652:9-652:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (740:9-740:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (691:9-691:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (787:9-787:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (695:9-695:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: all_sequences_to_align (550:9-550:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (740:9-740:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (903:9-903:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (744:9-744:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (427:9-427:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (787:9-787:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (483:9-483:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid_db (791:9-791:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (515:9-515:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: all_sequences_to_align (550:9-550:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (596:9-596:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (903:9-903:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (938:9-938:48)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: annotated_merged_fa (907:9-907:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1235:9-1235:44)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (427:9-427:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1236:9-1236:41)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads (483:9-483:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1237:9-1237:37)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (515:9-515:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1070:9-1070:27)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (596:9-596:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1156:9-1156:38)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembled_reads_fa (598:9-598:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (551:9-551:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (938:9-938:48)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (597:9-597:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_fasta (942:9-942:48)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1029:9-1029:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1235:9-1235:44)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1109:9-1109:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (1239:9-1239:44)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (734:9-734:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1236:9-1236:41)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (781:9-781:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (1240:9-1240:41)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (984:9-984:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1237:9-1237:37)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (598:9-598:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (1241:9-1241:37)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1034:9-1034:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1070:9-1070:27)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1072:9-1072:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contigs_fasta (1074:9-1074:27)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1116:9-1116:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1156:9-1156:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (114:9-114:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (1160:9-1160:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1157:9-1157:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (551:9-551:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1195:9-1195:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (597:9-597:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1239:9-1239:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (599:9-599:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (171:9-171:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1029:9-1029:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (203:9-203:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1033:9-1033:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (266:9-266:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1109:9-1109:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (1113:9-1113:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (333:9-333:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (734:9-734:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (391:9-391:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (738:9-738:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (428:9-428:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (781:9-781:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (485:9-485:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (785:9-785:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (984:9-984:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (53:9-53:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (988:9-988:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (598:9-598:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (603:9-603:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (600:9-600:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (649:9-649:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_wdl_version (604:9-604:35)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (692:9-692:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1034:9-1034:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (742:9-742:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1038:9-1038:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (789:9-789:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1072:9-1072:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1076:9-1076:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (873:9-873:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1116:9-1116:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (8:9-8:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1120:9-1120:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (907:9-907:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (114:9-114:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (939:9-939:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1157:9-1157:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (989:9-989:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1161:9-1161:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: guppy_basecaller_setting (331:9-331:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1195:9-1195:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (111:9-111:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1199:9-1199:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (170:9-170:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1239:9-1239:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (200:9-200:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (1243:9-1243:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (264:9-264:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (171:9-171:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (301:9-301:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (203:9-203:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (330:9-330:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (266:9-266:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (426:9-426:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (302:9-302:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (52:9-52:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (333:9-333:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (7:9-7:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (391:9-391:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (825:9-825:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (428:9-428:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1194:9-1194:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (485:9-485:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (112:9-112:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (516:9-516:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (201:9-201:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (53:9-53:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1028:9-1028:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (558:9-558:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1108:9-1108:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (559:9-559:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (647:9-647:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (603:9-603:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (690:9-690:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (606:9-606:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (739:9-739:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (649:9-649:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (786:9-786:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (653:9-653:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (906:9-906:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (692:9-692:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (983:9-983:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (696:9-696:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (600:9-600:34)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (742:9-742:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (554:9-554:35)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (746:9-746:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (741:9-741:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (789:9-789:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (788:9-788:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (793:9-793:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (552:9-552:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (829:9-829:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_host_db (113:9-113:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (833:9-833:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_human_db (202:9-202:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (873:9-873:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_contig_reads_fa (514:9-514:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (877:9-877:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1106:9-1106:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (8:9-8:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1027:9-1027:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (907:9-907:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1105:9-1105:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (911:9-911:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (827:9-827:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (939:9-939:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (905:9-905:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (943:9-943:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (689:9-689:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (989:9-989:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1026:9-1026:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (993:9-993:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1104:9-1104:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: guppy_basecaller_setting (331:9-331:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (872:9-872:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (111:9-111:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (779:9-779:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (170:9-170:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1102:9-1102:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (200:9-200:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1101:9-1101:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (264:9-264:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1233:9-1233:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (301:9-301:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (826:9-826:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (330:9-330:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (904:9-904:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (426:9-426:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (982:9-982:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (52:9-52:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1238:9-1238:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_fastq (7:9-7:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (646:9-646:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (825:9-825:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1100:9-1100:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: input_file (829:9-829:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1232:9-1232:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1194:9-1194:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (871:9-871:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (1198:9-1198:31)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (981:9-981:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (112:9-112:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1234:9-1234:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: library_type (201:9-201:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (732:9-732:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1028:9-1028:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: polishing_iterations (332:9-332:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1032:9-1032:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (870:9-870:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1108:9-1108:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (555:9-555:22)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (1112:9-1112:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1071:9-1071:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (647:9-647:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1025:9-1025:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (651:9-651:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (733:9-733:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (690:9-690:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (780:9-780:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (694:9-694:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (980:9-980:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (739:9-739:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (390:9-390:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (743:9-743:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (484:9-484:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (786:9-786:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_sam (389:9-389:34)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (790:9-790:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (828:9-828:34)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (906:9-906:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (553:9-553:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (910:9-910:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (599:9-599:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (983:9-983:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (557:9-557:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (987:9-987:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (602:9-602:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (600:9-600:34)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsample_depth (265:9-265:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (602:9-602:34)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1031:9-1031:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (554:9-554:35)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1111:9-1111:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (741:9-741:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (736:9-736:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (745:9-745:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (783:9-783:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (788:9-788:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (986:9-986:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_alignment_length (792:9-792:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1030:9-1030:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (552:9-552:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1110:9-1110:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_wdl_version (557:9-557:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (735:9-735:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_host_db (113:9-113:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (782:9-782:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap_human_db (202:9-202:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (985:9-985:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: non_contig_reads_fa (514:9-514:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1032:9-1032:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1106:9-1106:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1113:9-1113:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (1110:9-1110:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (737:9-737:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1027:9-1027:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (784:9-784:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1031:9-1031:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (987:9-987:40)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1105:9-1105:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1033:9-1033:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (1109:9-1109:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1114:9-1114:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (827:9-827:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (738:9-738:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (831:9-831:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (785:9-785:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (905:9-905:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (988:9-988:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hit_summary (909:9-909:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1288:9-1288:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (689:9-689:19)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1292:9-1292:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (693:9-693:19)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1300:9-1300:43)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1026:9-1026:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1299:9-1299:27)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1030:9-1030:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1285:9-1285:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1104:9-1104:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1268:9-1268:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (1108:9-1108:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1275:9-1275:48)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (872:9-872:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1272:9-1272:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8_reassigned (876:9-876:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1274:9-1274:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (779:9-779:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1287:9-1287:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_top_m8 (783:9-783:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1291:9-1291:33)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1102:9-1102:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1296:9-1296:61)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (1106:9-1106:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1295:9-1295:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1101:9-1101:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1284:9-1284:37)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1105:9-1105:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1297:9-1297:41)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1233:9-1233:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1279:9-1279:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (1237:9-1237:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1280:9-1280:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (826:9-826:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1293:9-1293:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (830:9-830:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1282:9-1282:37)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (904:9-904:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1270:9-1270:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (908:9-908:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1277:9-1277:38)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (982:9-982:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1289:9-1289:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hit_summary (986:9-986:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1290:9-1290:113)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1238:9-1238:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1302:9-1302:47)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (1242:9-1242:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1303:9-1303:44)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (646:9-646:19)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1023:6-1023:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (650:9-650:19)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1026:14-1026:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1100:9-1100:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1068:6-1068:27)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1104:9-1104:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1098:6-1098:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1232:9-1232:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (109:6-109:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (1236:9-1236:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1100:14-1100:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (871:9-871:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1104:14-1104:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (875:9-875:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1143:14-1143:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (981:9-981:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1144:14-1144:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8_reassigned (985:9-985:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1154:6-1154:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1234:9-1234:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1192:6-1192:17)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (1238:9-1238:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1230:6-1230:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (732:9-732:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1232:14-1232:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_top_m8 (736:9-736:23)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1234:14-1234:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: polishing_iterations (332:9-332:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1270:17-1270:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (870:9-870:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1284:15-1284:37)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: pre_alignment_fasta (874:9-874:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1288:14-1288:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (555:9-555:22)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1295:17-1295:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1071:9-1071:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1296:16-1296:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_contig_sam (1075:9-1075:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1297:16-1297:31)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1025:9-1025:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1616:14-1616:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (1029:9-1029:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (1618:14-1618:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (733:9-733:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (168:6-168:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (737:9-737:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:20)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (780:9-780:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (262:6-262:20)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (784:9-784:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (299:6-299:22)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (980:9-980:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (328:6-328:17)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: read_to_contig_tsv (984:9-984:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (387:6-387:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (390:9-390:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (424:6-424:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contig_tsv (484:9-484:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (481:6-481:27)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_sam (389:9-389:34)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (50:6-50:22)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (828:9-828:34)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (512:6-512:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads_to_contigs_tsv (832:9-832:34)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (548:6-548:20)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (553:9-553:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (552:16-552:29)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (599:9-599:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (554:15-554:35)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (601:9-601:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (557:17-557:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (557:9-557:26)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (586:14-586:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (558:9-558:26)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (594:6-594:20)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (602:9-602:26)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (5:6-5:22)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (605:9-605:26)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (602:17-602:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: subsample_depth (265:9-265:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (635:14-635:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1031:9-1031:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (644:6-644:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1035:9-1035:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (646:14-646:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1111:9-1111:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (648:14-648:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (1115:9-1115:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (678:14-678:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (736:9-736:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (687:6-687:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (740:9-740:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (689:14-689:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (783:9-783:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (691:14-691:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (787:9-787:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (721:14-721:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (986:9-986:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (730:6-730:21)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (990:9-990:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (732:14-732:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1030:9-1030:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (740:14-740:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1034:9-1034:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (767:14-767:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1110:9-1110:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (777:6-777:21)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (1114:9-1114:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (779:14-779:23)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (735:9-735:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (787:14-787:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (739:9-739:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (814:14-814:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (782:9-782:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (823:6-823:19)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (786:9-786:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (868:6-868:28)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (985:9-985:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (871:14-871:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_whitelist (989:9-989:29)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (872:14-872:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1032:9-1032:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (901:6-901:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1036:9-1036:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (936:6-936:26)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1113:9-1113:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (978:6-978:24)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (1117:9-1117:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (981:14-981:30)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (737:9-737:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_chunk (31:9-31:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (741:9-741:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (32:9-32:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (784:9-784:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (30:9-30:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (788:9-788:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_0 (28:9-28:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (987:9-987:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_1 (29:9-29:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (991:9-991:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: db_chunk (8:9-8:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1033:9-1033:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (9:9-9:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1037:9-1037:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extra_args (7:9-7:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1114:9-1114:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_0 (5:9-5:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (1118:9-1118:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_1 (6:9-6:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (738:9-738:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (26:6-26:17)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (742:9-742:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W001::Style/Low] line contains only whitespace (307:1-307:4)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (785:9-785:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W001::Style/Low] trailing space (53:139)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (789:9-789:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession_ids (115:9-115:36)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (988:9-988:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: clusters_directory (274:9-274:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (992:9-992:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cut_height (245:9-245:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1288:9-1288:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: distances (327:9-327:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (1292:9-1292:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (120:9-120:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1292:9-1292:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (190:9-190:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (1296:9-1296:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (210:9-210:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1300:9-1300:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:9-247:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (1304:9-1304:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (277:9-277:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1299:9-1299:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (329:9-329:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (1303:9-1303:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (352:9-352:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1285:9-1285:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (375:9-375:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (1289:9-1289:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (397:9-397:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_wdl_version (1306:9-1306:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: newick (373:9-373:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1268:9-1268:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (119:9-119:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (1272:9-1272:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (118:9-118:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1275:9-1275:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (117:9-117:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: guppy_basecaller_setting (1279:9-1279:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (116:9-116:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1272:9-1272:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_accession_ids (396:9-396:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: input_fastq (1276:9-1276:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_taxon_id (188:9-188:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1274:9-1274:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_and_reference_fastas (208:9-208:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: library_type (1278:9-1278:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (189:9-189:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1287:9-1287:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (246:9-246:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (1291:9-1291:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (328:9-328:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1291:9-1291:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (351:9-351:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (1295:9-1295:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (374:9-374:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1296:9-1296:61)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_align_p (276:9-276:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (1300:9-1300:61)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_distances (244:9-244:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1295:9-1295:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_hashes (275:9-275:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (1299:9-1299:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: superkingdom_name (209:9-209:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1284:9-1284:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variants (350:9-350:22)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (1288:9-1288:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_reference_accession_ids (19:9-19:62)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1297:9-1297:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cut_height (26:9-26:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (1301:9-1301:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (28:9-28:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_wdl_version (1307:9-1307:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (24:9-24:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1279:9-1279:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (23:9-23:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_host_db (1283:9-1283:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (22:9-22:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1280:9-1280:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (21:9-21:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap_human_db (1284:9-1284:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_taxon_id (14:9-14:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1293:9-1293:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (31:9-31:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (1297:9-1297:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples (13:9-13:34)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1282:9-1282:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ska_align_p (27:9-27:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: polishing_iterations (1286:9-1286:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: superkingdom_name (16:9-16:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1270:9-1270:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (113:6-113:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (1274:9-1274:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (116:16-116:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1277:9-1277:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (118:16-118:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: subsample_depth (1281:9-1281:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (177:6-177:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1289:9-1289:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (206:6-206:12)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (1293:9-1293:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1290:9-1290:113)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (23:16-23:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_whitelist (1294:9-1294:113)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (242:6-242:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1302:9-1302:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (272:6-272:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (1309:9-1309:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1303:9-1303:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (325:6-325:31)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (1310:9-1310:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (348:6-348:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1023:6-1023:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (371:6-371:28)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1026:14-1026:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (394:6-394:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1027:6-1027:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (162:5-162:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1030:14-1030:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (163:5-163:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1068:6-1068:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (164:5-164:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1072:6-1072:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:5-121:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1098:6-1098:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (157:5-157:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:6-109:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (193:5-193:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1100:14-1100:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (36:5-36:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1102:6-1102:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1104:14-1104:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:5-76:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1108:14-1108:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (197:5-197:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1143:14-1143:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (123:5-123:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1144:14-1144:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (195:5-195:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1147:14-1147:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (124:5-124:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1148:14-1148:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (165:5-165:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1154:6-1154:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (78:5-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1158:6-1158:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (10:5-10:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1192:6-1192:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (196:5-196:49)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1196:6-1196:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (92:5-92:17)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1230:6-1230:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (166:5-166:20)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1232:14-1232:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (93:5-93:19)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1234:14-1234:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (161:5-161:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1234:6-1234:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (160:5-160:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1236:14-1236:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (159:5-159:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1238:14-1238:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_bed (126:5-126:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1270:17-1270:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_db (125:5-125:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1274:17-1274:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:5-122:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1284:15-1284:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (158:5-158:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1288:14-1288:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (194:5-194:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1288:15-1288:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (37:5-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1292:14-1292:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1295:17-1295:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (77:5-77:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1296:16-1296:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_fasta (38:5-38:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1297:16-1297:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nr_fasta (89:5-89:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1299:17-1299:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nt_fasta (87:5-87:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1300:16-1300:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nr_fasta (85:5-85:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1301:16-1301:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nt_fasta (83:5-83:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1307:16-1307:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nr_fasta (81:5-81:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1616:14-1616:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nt_fasta (79:5-79:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1618:14-1618:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_annotated_merged_fa (7:5-7:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1625:14-1625:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_gsnap_hitsummary_tab (8:5-8:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (1627:14-1627:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_rapsearch2_hitsummary_tab (9:5-9:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:6-168:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_combined_json (91:5-91:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nr_json (90:5-90:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (262:6-262:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nt_json (88:5-88:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:6-299:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nr_json (86:5-86:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (328:6-328:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nt_json (84:5-84:39)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:6-387:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nr_json (82:5-82:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (424:6-424:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nt_json (80:5-80:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:6-481:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (198:5-198:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:6-50:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (234:5-234:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:6-512:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (235:5-235:37)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (548:6-548:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (236:5-236:33)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (552:16-552:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (225:5-225:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:15-554:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (240:5-240:32)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:16-557:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (237:5-237:18)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:17-557:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (238:5-238:19)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (558:17-558:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (241:5-241:30)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:14-586:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (588:14-588:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (245:5-245:90)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (594:6-594:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (596:6-596:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (242:5-242:76)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (5:6-5:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (244:5-244:89)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (602:17-602:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (605:17-605:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (635:14-635:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (639:14-639:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (644:6-644:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (646:14-646:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (648:14-648:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (648:6-648:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (650:14-650:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (652:14-652:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (678:14-678:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (248:5-248:40)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (682:14-682:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:14)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (687:6-687:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (122:12-122:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (689:14-689:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (143:10-143:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (691:14-691:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (144:10-144:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (691:6-691:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (147:10-147:41)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (693:14-693:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:25)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (695:14-695:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (158:12-158:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (721:14-721:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (159:10-159:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (725:14-725:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (730:6-730:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (732:14-732:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (165:10-165:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (734:6-734:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:18)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (736:14-736:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (194:12-194:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (740:14-740:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (744:14-744:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (767:14-767:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (226:12-226:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (771:14-771:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (777:6-777:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (779:14-779:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:46)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (781:6-781:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (232:10-232:48)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (783:14-783:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (233:10-233:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (787:14-787:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (343:10-343:27)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (791:14-791:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (344:10-344:56)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (814:14-814:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (345:10-345:60)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (818:14-818:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (346:10-346:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (823:6-823:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:43)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (827:6-827:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:51)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (868:6-868:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (871:14-871:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (34:6-34:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (872:14-872:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:44)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (872:6-872:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (353:11-353:45)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (875:14-875:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (876:14-876:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (901:6-901:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (905:6-905:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (74:6-74:26)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (936:6-936:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (77:12-77:21)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (940:6-940:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (78:10-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (978:6-978:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:50)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (981:14-981:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (351:5-351:23)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (982:6-982:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (868:5-868:13)" +document = "chanzuckerberg/czid-workflows:workflows/long-read-mngs/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (985:14-985:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered1_fastq (349:5-349:38)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_chunk (31:9-31:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered2_fastq (350:5-350:39)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (32:9-32:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered1_fastq (626:5-626:38)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: extra_args (30:9-30:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered2_fastq (627:5-627:39)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_0 (28:9-28:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered1_fastq (795:5-795:39)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: query_1 (29:9-29:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered2_fastq (796:5-796:40)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: db_chunk (8:9-8:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (259:5-259:54)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (9:9-9:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (543:5-543:54)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: extra_args (7:9-7:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (724:5-724:54)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_0 (5:9-5:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (262:5-262:17)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: query_1 (6:9-6:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (359:5-359:17)" +document = "chanzuckerberg/czid-workflows:workflows/minimap2/minimap2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:6-26:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (428:5-428:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W001::Style/Low] line contains only whitespace (307:1-307:4)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (546:5-546:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W001::Style/Low] trailing space (53:139)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (634:5-634:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession_ids (115:9-115:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (727:5-727:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: clusters_directory (274:9-274:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (803:5-803:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cut_height (245:9-245:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup1_fastq (947:5-947:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: distances (327:9-327:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup2_fastq (948:5-948:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (120:9-120:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (220:5-220:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (190:9-190:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (261:5-261:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (210:9-210:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (358:5-358:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (247:9-247:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (427:5-427:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (277:9-277:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:5-545:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (329:9-329:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (633:5-633:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (352:9-352:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (726:5-726:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (375:9-375:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (802:5-802:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (397:9-397:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (869:5-869:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: newick (373:9-373:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (913:5-913:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (119:9-119:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (952:5-952:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_s3_path (118:9-118:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (949:5-949:37)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (117:9-117:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_index_tar (258:5-258:24)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_s3_path (116:9-116:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (419:5-419:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_accession_ids (396:9-396:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (538:5-538:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reference_taxon_id (188:9-188:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (420:5-420:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: sample_and_reference_fastas (208:9-208:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (539:5-539:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (189:9-189:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp_options (354:5-356:82)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (246:9-246:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (216:5-216:20)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (328:9-328:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered1_fastq (911:5-911:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (351:9-351:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered2_fastq (912:5-912:33)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: samples (374:9-374:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered1_fastq (719:5-719:37)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_align_p (276:9-276:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered2_fastq (720:5-720:38)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_distances (244:9-244:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (631:5-631:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ska_hashes (275:9-275:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (800:5-800:31)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: superkingdom_name (209:9-209:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (542:5-542:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: variants (350:9-350:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (630:5-630:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: additional_reference_accession_ids (19:9-19:62)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (723:5-723:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cut_height (26:9-26:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (799:5-799:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (28:9-28:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_idx (421:5-421:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (24:9-24:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_options (425:5-425:54)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_s3_path (23:9-23:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (218:5-218:28)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (22:9-22:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (950:5-950:32)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_s3_path (21:9-21:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads1_fastq (214:5-214:22)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: reference_taxon_id (14:9-14:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads2_fastq (215:5-215:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (31:9-31:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (221:5-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: samples (13:9-13:34)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (914:5-914:21)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ska_align_p (27:9-27:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (953:5-953:21)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: superkingdom_name (16:9-16:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input1_fastq (254:5-254:28)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (113:6-113:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input2_fastq (255:5-255:29)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:16-116:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (14:5-14:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:16-118:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_index_tar (17:5-17:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (177:6-177:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cpu (32:5-32:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (206:6-206:12)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (33:5-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_index_tar (27:5-27:117)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (23:16-23:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (10:5-10:18)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:6-242:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (11:5-11:19)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (272:6-272:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (36:5-36:30)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:16-31:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gtf_gz (22:5-22:17)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (325:6-325:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_index_tar (18:5-18:26)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:6-348:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (16:5-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (371:6-371:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_index_tar (24:5-24:33)" +document = "chanzuckerberg/czid-workflows:workflows/phylotree-ng/run.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:6-394:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_hisat2_index_tar (25:5-25:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (126:5-126:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kallisto_idx (19:5-19:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_coverage_json (162:5-162:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (29:5-29:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (127:5-127:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (30:5-30:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contig_stats_json (163:5-163:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (12:5-12:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (128:5-128:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (37:5-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: contig_in_contigs_fasta (164:5-164:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (133:8-133:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:5-121:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (134:9-134:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (157:5-157:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (193:5-193:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (162:11-162:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (36:5-36:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (166:10-166:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (167:11-167:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:5-76:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (168:10-168:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (161:5-161:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (169:10-169:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_clusters_csv (197:5-197:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (171:10-171:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (123:5-123:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (172:11-172:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (159:5-159:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (178:10-178:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastqs (195:5-195:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (17:10-17:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (124:5-124:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (129:5-129:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (182:11-182:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (165:5-165:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (183:10-183:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8_gsnap_deduped_m8 (78:5-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (184:10-184:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (10:5-10:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (160:5-160:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (186:11-186:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nonhost_fasta_refined_taxid_annot_fasta (196:5-196:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (187:10-187:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (92:5-92:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (18:10-18:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (130:5-130:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (192:11-192:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_info_db (166:5-166:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (193:11-193:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (93:5-93:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (194:11-194:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (125:5-125:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (195:11-195:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_blast_top_m8 (161:5-161:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (196:11-196:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (124:5-124:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (197:11-197:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_hitsummary2_tab (160:5-160:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (123:5-123:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (200:11-200:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: refined_gsnap_in_gsnap_reassigned_m8 (159:5-159:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (212:6-212:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_bed (126:5-126:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: resist_genome_db (125:5-125:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:5-122:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (221:12-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (158:5-158:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (239:10-239:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (194:5-194:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (240:11-240:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (37:5-37:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (24:10-24:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (251:6-251:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (77:5-77:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (254:10-254:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_fasta (38:5-38:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (255:11-255:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nr_fasta (89:5-89:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (259:12-259:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_family_nt_fasta (87:5-87:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (25:10-25:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nr_fasta (85:5-85:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (267:10-267:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_genus_nt_fasta (83:5-83:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (331:10-331:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nr_fasta (81:5-81:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (332:10-332:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_annot_sorted_nt_fasta (79:5-79:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (333:11-333:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_annotated_merged_fa (7:5-7:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (349:10-349:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_gsnap_hitsummary_tab (8:5-8:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_fasta_in_rapsearch2_hitsummary_tab (9:5-9:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_combined_json (91:5-91:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (404:10-404:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nr_json (90:5-90:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (405:11-405:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_family_nt_json (88:5-88:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (419:10-419:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nr_json (86:5-86:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (420:11-420:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_genus_nt_json (84:5-84:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (524:10-524:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nr_json (82:5-82:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (535:6-535:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxid_locations_nt_json (80:5-80:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (538:10-538:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (162:5-162:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (539:11-539:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (198:5-198:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (543:12-543:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (198:5-198:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (551:10-551:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_coverage_json (234:5-234:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (611:10-611:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (199:5-199:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (612:11-612:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contig_stats_json (235:5-235:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (623:6-623:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (200:5-200:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (626:10-626:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: contig_in_contigs_fasta (236:5-236:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (627:11-627:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (189:5-189:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (631:12-631:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (225:5-225:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (639:10-639:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (204:5-204:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (699:10-699:37)" - +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_clusters_csv (240:5-240:32)" + [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (700:11-700:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (201:5-201:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (716:6-716:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (237:5-237:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (719:10-719:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (202:5-202:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (720:11-720:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (238:5-238:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (724:12-724:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (205:5-205:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (732:10-732:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (241:5-241:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (780:10-780:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (194:5-194:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (781:11-781:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_m8_gsnap_deduped_m8 (230:5-230:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (792:6-792:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (209:5-209:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (795:10-795:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (245:5-245:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (796:11-796:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (203:5-203:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (800:12-800:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nonhost_fasta_refined_taxid_annot_fasta (239:5-239:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (808:10-808:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (206:5-206:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (855:10-855:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (242:5-242:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (856:11-856:39)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (208:5-208:89)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (909:6-909:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_info_db (244:5-244:89)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (911:10-911:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (207:5-207:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (912:11-912:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (243:5-243:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (914:12-914:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (197:5-197:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (932:10-932:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_blast_top_m8 (233:5-233:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (933:11-933:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (196:5-196:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (945:6-945:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_hitsummary2_tab (232:5-232:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (947:10-947:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (195:5-195:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (948:11-948:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: refined_gsnap_in_gsnap_reassigned_m8 (231:5-231:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (953:12-953:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (211:5-211:83)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (19:9-19:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_bed (247:5-247:83)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (18:9-18:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (210:5-210:80)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (14:9-14:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: resist_genome_db (246:5-246:80)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (15:9-15:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (190:5-190:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (16:9-16:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (226:5-226:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (17:9-17:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (191:5-191:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: non_host_gsnap_genome_name (20:9-20:53)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_annotated_merged_fa (227:5-227:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (21:9-21:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (192:5-192:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (17:14-17:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_gsnap_hitsummary_tab (228:5-228:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (193:5-193:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (123:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxid_fasta_in_rapsearch2_hitsummary_tab (229:5-229:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (131:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (212:5-212:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (132:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (248:5-248:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (137:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:14)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (171:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (227:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:12-122:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (307:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (123:10-123:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (308:19)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:10-124:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (318:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:10-125:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (332:11)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (129:10-129:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (342:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (143:10-143:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (75:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (144:10-144:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W001::Style/Low] trailing space (78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (147:10-147:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (169:9-169:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (225:9-225:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (155:6-155:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (174:9-174:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:12-158:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (230:9-230:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (159:10-159:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (7:5-7:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (44:5-44:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (122:9-122:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:10-165:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (74:9-74:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (178:10-178:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (168:9-168:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (179:11-179:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (224:9-224:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (190:12-190:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (123:9-123:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (191:6-191:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (119:9-119:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:10-193:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (173:9-173:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:10-194:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (229:9-229:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:12-194:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (33:5-33:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:10-195:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:10-196:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:9-76:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:10-197:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (170:9-170:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (226:9-226:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (45:5-45:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (226:12-226:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (121:9-121:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (73:9-73:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_counts_with_dcr_json (39:5-39:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_deduped_m8 (37:5-37:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (232:10-232:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_hitsummary_tab (38:5-38:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (233:10-233:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8 (36:5-36:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:10-299:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (35:5-35:48)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (300:11-300:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (166:9-166:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (343:10-343:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (222:9-222:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (344:10-344:56)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (125:9-125:34)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:10-345:60)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (78:9-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (346:10-346:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (165:9-165:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (221:9-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:51)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (172:9-172:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (228:9-228:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:6-34:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (75:9-75:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (126:9-126:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (353:11-353:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (171:9-171:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (227:9-227:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (79:9-79:22)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_counts_with_dcr_json (43:5-43:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:6-74:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_deduped_m8 (41:5-41:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:12-77:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_hitsummary_tab (42:5-42:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:10-78:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_m8 (40:5-40:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/experimental.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (9:10-9:50)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (124:9-124:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: adapter_fasta (351:5-351:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (77:9-77:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bam (868:5-868:13)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (120:9-120:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered1_fastq (349:5-349:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (175:9-175:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_ercc_filtered2_fastq (350:5-350:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (231:9-231:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered1_fastq (626:5-626:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (34:5-34:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_host_filtered2_fastq (627:5-627:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered1_fastq (795:5-795:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (72:9-72:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_human_filtered2_fastq (796:5-796:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (167:9-167:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (259:5-259:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (223:9-223:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (543:5-543:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (286:5-286:105)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: bowtie2_options (724:5-724:54)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (293:5-293:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (262:5-262:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (283:5-283:47)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (359:5-359:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (290:5-290:101)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (428:5-428:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (302:5-302:42)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (546:5-546:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (300:5-300:79)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (634:5-634:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (296:5-296:32)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (727:5-727:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (304:5-304:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cpu (803:5-803:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (277:5-277:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup1_fastq (947:5-947:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (282:5-282:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: dedup2_fastq (948:5-948:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (279:5-279:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (220:5-220:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (280:5-280:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (261:5-261:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (281:5-281:49)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (358:5-358:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (288:5-288:44)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (427:5-427:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (284:5-284:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (545:5-545:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (285:5-285:90)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (633:5-633:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (297:5-297:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (726:5-726:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (294:5-294:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (802:5-802:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (298:5-298:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (869:5-869:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (289:5-289:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (913:5-913:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (301:5-301:52)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (952:5-952:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (299:5-299:94)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (949:5-949:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (295:5-295:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: ercc_index_tar (258:5-258:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (303:5-303:37)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (419:5-419:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (278:5-278:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp1_fastq (538:5-538:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (287:5-287:97)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (420:5-420:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (291:5-291:43)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp2_fastq (539:5-539:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (292:5-292:40)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastp_options (354:5-356:82)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: file_ext (216:5-216:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (117:6-117:30)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered1_fastq (911:5-911:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (120:16-120:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_filtered2_fastq (912:5-912:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (154:14-154:20)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered1_fastq (719:5-719:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (163:6-163:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_host_filtered2_fastq (720:5-720:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (631:5-631:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: hisat2_options (800:5-800:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (542:5-542:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (630:5-630:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (723:5-723:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: index_tar (799:5-799:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_idx (421:5-421:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: kallisto_options (425:5-425:54)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_input_fragments (218:5-218:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: max_subsample_fragments (950:5-950:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads1_fastq (214:5-214:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: reads2_fastq (215:5-215:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (221:5-221:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (914:5-914:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (953:5-953:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input1_fastq (254:5-254:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: valid_input2_fastq (255:5-255:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: adapter_fasta (14:5-14:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: bowtie2_index_tar (17:5-17:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: cpu (32:5-32:17)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (33:5-33:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: ercc_index_tar (27:5-27:117)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (10:5-10:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (11:5-11:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: file_ext (36:5-36:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gtf_gz (22:5-22:17)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: hisat2_index_tar (18:5-18:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_genome (16:5-16:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_bowtie2_index_tar (24:5-24:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: human_hisat2_index_tar (25:5-25:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: kallisto_idx (19:5-19:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_input_fragments (29:5-29:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: max_subsample_fragments (30:5-30:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nucleotide_type (12:5-12:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (37:5-37:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (133:8-133:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (134:9-134:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (161:10-161:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (162:11-162:48)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:10-166:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (167:11-167:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:10-168:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:10-169:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (171:10-171:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (172:11-172:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (178:10-178:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:10-17:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (182:11-182:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (183:10-183:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (184:10-184:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (186:11-186:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (187:10-187:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (18:10-18:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (192:11-192:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:11-193:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (194:11-194:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (195:11-195:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:11-196:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:11-197:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:11-200:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (212:6-212:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (214:10-214:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (215:11-215:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (221:12-221:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:10-239:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (240:11-240:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (24:10-24:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (251:6-251:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (254:10-254:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (255:11-255:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (259:12-259:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (25:10-25:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (267:10-267:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (331:10-331:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (332:10-332:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (333:11-333:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:10-349:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:12-37:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (404:10-404:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (405:11-405:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (419:10-419:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (420:11-420:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (524:10-524:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (535:6-535:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:10-538:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (539:11-539:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (543:12-543:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (551:10-551:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (611:10-611:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (612:11-612:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (623:6-623:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (626:10-626:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (627:11-627:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (631:12-631:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (639:10-639:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (699:10-699:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (700:11-700:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (716:6-716:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (719:10-719:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (720:11-720:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (724:12-724:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (732:10-732:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (780:10-780:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (781:11-781:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (792:6-792:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (795:10-795:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (796:11-796:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (800:12-800:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (808:10-808:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (855:10-855:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (856:11-856:39)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (909:6-909:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (911:10-911:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (912:11-912:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (914:12-914:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (932:10-932:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (933:11-933:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (945:6-945:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (947:10-947:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (948:11-948:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/host_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (953:12-953:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (19:9-19:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (18:9-18:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (14:9-14:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_0 (15:9-15:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: fastqs_1 (16:9-16:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (17:9-17:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: non_host_gsnap_genome_name (20:9-20:53)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (21:9-21:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (17:14-17:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/local_driver.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (21:16-21:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (123:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (125:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (131:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (132:48)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (134:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (135:48)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (137:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (140:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (171:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (175:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (227:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (231:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (307:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (308:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (313:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (314:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (318:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (325:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (332:11)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (339:11)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (342:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (350:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (75:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W001::Style/Low] trailing space (78:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (169:9-169:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (173:9-173:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (225:9-225:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (229:9-229:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (174:9-174:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (178:9-178:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (230:9-230:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: count_type (234:9-234:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (7:5-7:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (44:5-44:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (122:9-122:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (124:9-124:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: db_path (74:9-74:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (168:9-168:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (172:9-172:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (224:9-224:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (228:9-228:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (123:9-123:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_args (125:9-125:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: diamond_wdl_version (129:9-129:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (119:9-119:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (121:9-121:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (173:9-173:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (177:9-177:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (229:9-229:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (233:9-233:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (33:5-33:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (76:9-76:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (170:9-170:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (174:9-174:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (226:9-226:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_size (230:9-230:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (45:5-45:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (121:9-121:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (123:9-123:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: fastas (73:9-73:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_counts_with_dcr_json (39:5-39:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_deduped_m8 (37:5-37:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_hitsummary_tab (38:5-38:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_m8 (36:5-36:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (35:5-35:48)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (166:9-166:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (170:9-170:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (222:9-222:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (226:9-226:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (125:9-125:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_diamond_index (127:9-127:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: local_minimap2_index (78:9-78:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (165:9-165:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (169:9-169:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (221:9-221:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: m8_file (225:9-225:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (172:9-172:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (176:9-176:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (228:9-228:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_read_length (232:9-232:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_args (75:9-75:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: minimap2_wdl_version (80:9-80:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (126:9-126:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (128:9-128:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (171:9-171:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (175:9-175:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (227:9-227:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (231:9-231:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: prefix (79:9-79:22)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_counts_with_dcr_json (43:5-43:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_deduped_m8 (41:5-41:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_hitsummary_tab (42:5-42:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_m8 (40:5-40:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (124:9-124:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (126:9-126:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: run_locally (77:9-77:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (120:9-120:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (122:9-122:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (175:9-175:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (179:9-179:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (231:9-231:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (235:9-235:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (34:5-34:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (72:9-72:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (167:9-167:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (171:9-171:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (223:9-223:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (227:9-227:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (286:5-286:105)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (290:5-290:105)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (293:5-293:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: alignment_scalability (297:5-297:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (283:5-283:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (287:5-287:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (290:5-290:101)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (294:5-294:101)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (302:5-302:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_args (306:5-306:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (300:5-300:79)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_db (304:5-304:79)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (296:5-296:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_local_db_path (300:5-300:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (304:5-304:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_prefix (308:5-308:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: diamond_wdl_version (310:5-310:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (277:5-277:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (281:5-281:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (282:5-282:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (286:5-286:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (279:5-279:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (283:5-283:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (280:5-280:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (284:5-284:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (281:5-281:49)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (285:5-285:49)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (288:5-288:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_dir_suffix (292:5-292:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (284:5-284:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (288:5-288:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (285:5-285:90)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (289:5-289:90)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (297:5-297:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_genome_name (301:5-301:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (294:5-294:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_gsnap_index (298:5-298:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (298:5-298:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: local_rapsearch2_index (302:5-302:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (289:5-289:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_read_length (293:5-293:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (301:5-301:52)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_args (305:5-305:52)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (299:5-299:94)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_db (303:5-303:94)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (295:5-295:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_local_db_path (299:5-299:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (303:5-303:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_prefix (307:5-307:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: minimap2_wdl_version (309:5-309:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (278:5-278:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (282:5-282:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (287:5-287:97)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (291:5-291:97)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (291:5-291:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (295:5-295:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (292:5-292:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (296:5-296:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:14-109:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:14-111:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:6-117:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:6-119:30)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:16-120:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (122:16-122:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (154:14-154:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (158:14-158:20)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (163:6-163:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (165:14-165:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (167:6-167:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (173:14-173:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (175:16-175:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (179:16-179:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (209:14-209:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (213:14-213:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (219:6-219:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (221:14-221:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (223:6-223:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (229:14-229:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:16-231:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (235:16-235:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (264:14-264:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (268:14-268:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (278:12-278:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (282:12-282:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (286:10-286:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (290:10-290:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (295:11-295:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (298:11-298:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:11-299:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (299:12-299:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (301:12-301:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (302:11-302:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (169:14-169:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (305:12-305:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (307:12-307:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (309:12-309:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (31:6-31:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:12-34:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:10-36:18)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:10-37:26)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (383:10-383:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (384:10-384:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (387:11-387:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:10-389:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (390:10-390:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:50)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:56)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:11-394:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (395:11-395:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (397:10-397:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (398:10-398:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (399:10-399:50)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (400:10-400:56)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (402:11-402:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:23)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:10-42:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:10-43:41)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (70:6-70:31)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:16-72:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (75:16-75:29)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (78:15-78:35)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:16-80:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (160:5-160:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (208:5-208:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (156:5-156:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (204:5-204:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (52:5-52:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (153:5-153:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (201:5-201:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (49:5-49:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (347:5-347:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (392:5-392:33)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (352:5-352:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (397:5-397:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (351:5-351:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (396:5-396:44)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (349:5-349:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (394:5-394:40)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (348:5-348:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (393:5-393:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nr_refseq_fasta (205:5-205:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nt_refseq_fasta (157:5-157:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (353:5-353:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (398:5-398:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (358:5-358:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (403:5-403:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (357:5-357:49)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (402:5-402:49)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (355:5-355:45)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (400:5-400:45)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (354:5-354:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (399:5-399:43)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (155:5-155:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (203:5-203:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (51:5-51:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_annotated_merged_fa (390:5-390:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (350:5-350:53)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (395:5-395:53)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (356:5-356:58)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (401:5-401:58)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_mapped_only_fasta (435:5-435:56)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_unidentified_fa (391:5-391:42)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (154:5-154:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (202:5-202:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (50:5-50:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes_tsv (250:5-250:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (290:5-290:34)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (359:5-359:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (162:5-162:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (254:5-254:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (113:5-113:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (147:5-147:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (195:5-195:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (241:5-241:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (288:5-288:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (316:5-316:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (344:5-344:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (388:5-388:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (433:5-433:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (47:5-47:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (79:5-79:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (158:5-158:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (206:5-206:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (360:5-360:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (8:5-8:37)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (152:5-152:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (84:5-84:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (150:5-150:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (82:5-82:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (151:5-151:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (175:16-175:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (83:5-83:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (209:14-209:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (149:5-149:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (219:6-219:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (81:5-81:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (221:14-221:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (346:5-346:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (225:14-225:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (7:5-7:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (231:16-231:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (318:5-318:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (264:14-264:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (119:5-119:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (278:12-278:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (159:5-159:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (286:10-286:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (207:5-207:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (295:11-295:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (252:5-252:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (298:11-298:33)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (404:5-404:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (299:12-299:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (87:5-87:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (301:12-301:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (9:5-9:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (303:12-303:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (249:5-249:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (31:6-31:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_db (121:5-121:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (34:12-34:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hitsummary2_tab (248:5-248:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (36:10-36:18)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (120:5-120:19)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (37:10-37:26)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (247:5-247:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (383:10-383:28)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (246:5-246:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (384:10-384:36)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (85:5-85:17)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (387:11-387:27)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hitsummary2_tab (245:5-245:28)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (86:5-86:19)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (244:5-244:15)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (118:5-118:56)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (200:5-200:56)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (116:5-116:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (198:5-198:46)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (117:5-117:50)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (199:5-199:50)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (115:5-115:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (197:5-197:38)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (114:5-114:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (148:5-148:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (196:5-196:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (242:5-242:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (289:5-289:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (317:5-317:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (345:5-345:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (389:5-389:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (434:5-434:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (48:5-48:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (80:5-80:21)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (161:5-161:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (209:5-209:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (253:5-253:25)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (163:5-163:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (256:5-256:36)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (164:5-164:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (210:5-210:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (257:5-257:32)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (494:5-494:131)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (487:5-487:47)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (496:5-496:101)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (473:5-473:27)" + +[[concerns]] +kind = "LintWarning" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (486:5-486:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (389:10-389:38)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_counts_with_dcr_json (481:5-481:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (390:10-390:46)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_deduped_m8 (479:5-479:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (391:10-391:50)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_hitsummary_tab (480:5-480:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:56)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_m8 (478:5-478:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (394:11-394:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (475:5-475:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:24)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (476:5-476:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (40:10-40:23)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (477:5-477:49)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (488:5-488:40)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (42:10-42:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (493:5-493:90)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (43:10-43:41)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (499:5-499:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_db (491:5-491:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (70:6-70:31)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (492:5-492:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (72:16-72:25)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (489:5-489:76)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (75:16-75:29)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (490:5-490:87)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/non_host_alignment.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (78:15-78:35)" +document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_counts_with_dcr_json (485:5-485:56)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (160:5-160:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_deduped_m8 (483:5-483:46)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: accession2taxid (208:5-208:25)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_hitsummary_tab (484:5-484:50)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (156:5-156:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_m8 (482:5-482:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (204:5-204:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (474:5-474:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contig_stats_json (52:5-52:36)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (495:5-495:97)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (153:5-153:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (497:5-497:43)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (201:5-201:32)" +message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (498:5-498:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_contigs_fasta (49:5-49:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (111:6-111:50)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (347:5-347:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (114:12-114:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_m8 (392:5-392:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (115:10-115:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (352:5-352:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (116:10-116:46)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_blast_top_m8 (397:5-397:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (117:10-117:50)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (351:5-351:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (118:10-118:56)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_contig_summary_json (396:5-396:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (145:6-145:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (349:5-349:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (148:12-148:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_hitsummary2_tab (394:5-394:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (149:10-149:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (348:5-348:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:10-150:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_gsnap_reassigned_m8 (393:5-393:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nr_refseq_fasta (205:5-205:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (180:10-180:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_nt_refseq_fasta (157:5-157:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (353:5-353:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (182:10-182:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_m8 (398:5-398:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (358:5-358:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (193:6-193:41)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_blast_top_m8 (403:5-403:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (196:12-196:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (357:5-357:49)" +message = "[v1::W006::Naming/Low] identifier must be snake case (197:10-197:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_contig_summary_json (402:5-402:49)" +message = "[v1::W006::Naming/Low] identifier must be snake case (198:10-198:46)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (355:5-355:45)" +message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:50)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_hitsummary2_tab (400:5-400:45)" +message = "[v1::W006::Naming/Low] identifier must be snake case (200:10-200:56)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (354:5-354:43)" +message = "[v1::W006::Naming/Low] identifier must be snake case (208:10-208:25)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_rapsearch2_reassigned_m8 (399:5-399:43)" +message = "[v1::W006::Naming/Low] identifier must be snake case (226:10-226:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (155:5-155:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (227:10-227:43)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (203:5-203:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (228:10-228:45)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_read_contig_sam (51:5-51:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:58)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_annotated_merged_fa (390:5-390:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:49)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (350:5-350:53)" +message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:42)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_gsnap_counts_with_dcr_json (395:5-395:53)" +message = "[v1::W006::Naming/Low] identifier must be snake case (239:6-239:30)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (356:5-356:58)" +message = "[v1::W006::Naming/Low] identifier must be snake case (242:12-242:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_rapsearch2_counts_with_dcr_json (401:5-401:58)" +message = "[v1::W006::Naming/Low] identifier must be snake case (244:10-244:15)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_taxid_annot_mapped_only_fasta (435:5-435:56)" +message = "[v1::W006::Naming/Low] identifier must be snake case (245:10-245:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_refined_unidentified_fa (391:5-391:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (247:10-247:15)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (154:5-154:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (248:10-248:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (202:5-202:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (275:10-275:19)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: assembly_scaffolds_fasta (50:5-50:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (276:10-276:32)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: cluster_sizes_tsv (250:5-250:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (286:6-286:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: counts_json_files (290:5-290:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (289:12-289:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: czid_dedup_out_duplicate_clusters_csv (359:5-359:47)" +message = "[v1::W006::Naming/Low] identifier must be snake case (314:6-314:17)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (162:5-162:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (317:12-317:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: deuterostome_db (254:5-254:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (342:6-342:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (113:5-113:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (345:12-345:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (147:5-147:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (195:5-195:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (241:5-241:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:10-349:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (288:5-288:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:37)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (316:5-316:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (353:10-353:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (344:5-344:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (354:10-354:43)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (388:5-388:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (355:10-355:45)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (433:5-433:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (356:10-356:58)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (47:5-47:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (357:10-357:49)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (5:5-5:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (358:10-358:42)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: docker_image_id (79:5-79:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (386:6-386:24)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (158:5-158:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (389:12-389:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (206:5-206:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:33)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (360:5-360:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (393:10-393:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: duplicate_cluster_sizes_tsv (8:5-8:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (394:10-394:40)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (152:5-152:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (397:10-397:37)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_counts_with_dcr_json (84:5-84:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (398:10-398:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (150:5-150:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (399:10-399:43)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_deduped_m8 (82:5-82:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:17)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (151:5-151:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (400:10-400:45)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_hitsummary_tab (83:5-83:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (401:10-401:58)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (149:5-149:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (402:10-402:49)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: gsnap_out_gsnap_m8 (81:5-81:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (403:10-403:42)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (346:5-346:48)" +message = "[v1::W006::Naming/Low] identifier must be snake case (431:6-431:26)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: host_filter_out_gsnap_filter_fa (7:5-7:48)" +message = "[v1::W006::Naming/Low] identifier must be snake case (434:12-434:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: json_files (318:5-318:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:6-45:27)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (119:5-119:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (474:12-474:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (159:5-159:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (478:10-478:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (207:5-207:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (479:10-479:36)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (252:5-252:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (482:10-482:38)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (404:5-404:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (483:10-483:46)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: lineage_db (87:5-87:20)" +message = "[v1::W006::Naming/Low] identifier must be snake case (484:10-484:50)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: min_contig_length (9:5-9:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (485:10-485:56)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_contig_summary_json (249:5-249:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:12-48:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_db (121:5-121:17)" +message = "[v1::W006::Naming/Low] identifier must be snake case (494:10-494:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_hitsummary2_tab (248:5-248:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (695:11-695:42)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_loc_db (120:5-120:19)" +message = "[v1::W006::Naming/Low] identifier must be snake case (696:10-696:51)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nr_m8 (247:5-247:15)" +message = "[v1::W006::Naming/Low] identifier must be snake case (697:10-697:56)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_contig_summary_json (246:5-246:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (698:10-698:58)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_db (85:5-85:17)" +message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_hitsummary2_tab (245:5-245:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (701:10-701:55)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_loc_db (86:5-86:19)" +message = "[v1::W006::Naming/Low] identifier must be snake case (703:10-703:61)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: nt_m8 (244:5-244:15)" +message = "[v1::W006::Naming/Low] identifier must be snake case (704:10-704:66)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (118:5-118:56)" +message = "[v1::W006::Naming/Low] identifier must be snake case (705:10-705:68)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_counts_with_dcr_json (200:5-200:56)" +message = "[v1::W006::Naming/Low] identifier must be snake case (706:10-706:81)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (116:5-116:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (707:10-707:72)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_deduped_m8 (198:5-198:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (708:10-708:65)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (117:5-117:50)" +message = "[v1::W006::Naming/Low] identifier must be snake case (709:11-709:39)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_hitsummary_tab (199:5-199:50)" +message = "[v1::W006::Naming/Low] identifier must be snake case (77:6-77:45)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (115:5-115:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (80:12-80:21)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: rapsearch2_out_rapsearch2_m8 (197:5-197:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (81:10-81:28)" [[concerns]] kind = "LintWarning" document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (114:5-114:21)" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:10-82:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (148:5-148:21)" +document = "stjudecloud/workflows:data_structures/flag_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (124:10-124:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (196:5-196:21)" +document = "stjudecloud/workflows:data_structures/flag_filter.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:6-71:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (242:5-242:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (143:6-143:24)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (289:5-289:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (32:12-32:14)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (317:5-317:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:13-33:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (345:5-345:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:13-34:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (389:5-389:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:13-35:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (434:5-434:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:13-36:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (48:5-48:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (37:13-37:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (6:5-6:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:13-38:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: s3_wd_uri (80:5-80:21)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (39:13-39:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (161:5-161:25)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (40:13-40:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (209:5-209:25)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:10-41:12)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: taxon_blacklist (253:5-253:25)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:13-42:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (163:5-163:36)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:13-43:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_deuterostome_filter (256:5-256:36)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:13-44:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (164:5-164:32)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:13-45:15)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (210:5-210:32)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (48:6-48:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within task: use_taxon_whitelist (257:5-257:32)" +document = "stjudecloud/workflows:data_structures/read_group.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (96:6-96:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: accession2taxid_db (494:5-494:131)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:17-119:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: czid_dedup_out_duplicate_clusters_csv (487:5-487:47)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (120:17-120:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: deuterostome_db (496:5-496:101)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (82:14-82:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: docker_image_id (473:5-473:27)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (83:14-83:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: duplicate_cluster_sizes_tsv (486:5-486:37)" +document = "stjudecloud/workflows:tools/cellranger.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (87:14-87:25)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_counts_with_dcr_json (481:5-481:46)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (139:11-139:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_deduped_m8 (479:5-479:36)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (140:11-140:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_hitsummary_tab (480:5-480:40)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (141:11-141:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: gsnap_out_gsnap_m8 (478:5-478:28)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (142:11-142:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_1_fa (475:5-475:43)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (149:12-149:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_2_fa (476:5-476:44)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (150:12-150:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: host_filter_out_gsnap_filter_merged_fa (477:5-477:49)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (151:12-151:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: index_version (488:5-488:40)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (152:12-152:18)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: lineage_db (493:5-493:90)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (166:14-166:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: min_contig_length (499:5-499:32)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (167:15-167:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_db (491:5-491:76)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (168:14-168:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nr_loc_db (492:5-492:87)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (169:15-169:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_db (489:5-489:76)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (71:11-71:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: nt_loc_db (490:5-490:87)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (72:11-72:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_counts_with_dcr_json (485:5-485:56)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (73:11-73:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_deduped_m8 (483:5-483:46)" +document = "stjudecloud/workflows:tools/fq.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (74:11-74:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_hitsummary_tab (484:5-484:50)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (107:14-107:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: rapsearch2_out_rapsearch2_m8 (482:5-482:38)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (108:14-108:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: s3_wd_uri (474:5-474:21)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (109:21-109:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: taxon_blacklist (495:5-495:97)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (249:14-249:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_deuterostome_filter (497:5-497:43)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (250:14-250:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W003::Completeness/Medium] missing parameter meta within workflow: use_taxon_whitelist (498:5-498:40)" +document = "stjudecloud/workflows:tools/gatk4.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:14-62:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (111:6-111:50)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (347:11-347:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (114:12-114:21)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (348:11-348:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (115:10-115:38)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (116:10-116:46)" +document = "stjudecloud/workflows:tools/kraken2.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (117:10-117:50)" +document = "stjudecloud/workflows:tools/librarian.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (30:11-30:21)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (118:10-118:56)" +document = "stjudecloud/workflows:tools/md5sum.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:14-36:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (145:6-145:36)" +document = "stjudecloud/workflows:tools/md5sum.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:20)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (148:12-148:21)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (119:15-119:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (149:10-149:28)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (121:15-121:39)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (150:10-150:36)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (325:14-325:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (160:10-160:25)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (327:14-327:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (180:10-180:33)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (420:14-420:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (181:10-181:38)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (422:14-422:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (182:10-182:40)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:14-481:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (185:10-185:37)" +document = "stjudecloud/workflows:tools/picard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (483:14-483:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (193:6-193:41)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (478:20-478:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (196:12-196:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (479:19-479:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (197:10-197:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (480:20-480:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (198:10-198:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (481:19-481:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (199:10-199:50)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (485:19-485:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (200:10-200:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (487:19-487:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (208:10-208:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (491:19-491:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (226:10-226:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (493:19-493:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (227:10-227:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (497:19-497:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (228:10-228:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (499:19-499:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (229:10-229:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (503:19-503:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (230:10-230:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (505:19-505:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (231:10-231:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (509:30-509:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (239:6-239:30)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (510:28-510:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (242:12-242:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:27-511:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (244:10-244:15)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (511:30-511:46)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (245:10-245:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:24-512:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (247:10-247:15)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (512:28-512:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (248:10-248:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (513:24-513:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (275:10-275:19)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (513:27-513:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (276:10-276:32)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (514:24-514:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (286:6-286:24)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (515:16-515:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (289:12-289:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (515:24-515:48)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (314:6-314:17)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (516:16-516:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (317:12-317:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (516:24-516:36)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (342:6-342:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (345:12-345:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:31)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (347:10-347:33)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (348:10-348:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (349:10-349:40)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:33)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (352:10-352:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (353:10-353:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (354:10-354:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (355:10-355:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:30)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (356:10-356:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (357:10-357:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (358:10-358:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:28)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (386:6-386:24)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (389:12-389:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (392:10-392:33)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (393:10-393:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (394:10-394:40)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (397:10-397:37)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (398:10-398:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (399:10-399:43)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (3:6-3:17)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:38)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (400:10-400:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (401:10-401:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (402:10-402:49)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:29)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (403:10-403:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (431:6-431:26)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (434:12-434:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:44)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (45:6-45:27)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (474:12-474:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:35)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (478:10-478:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (479:10-479:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (482:10-482:38)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:26)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (483:10-483:46)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (484:10-484:50)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (534:16-534:37)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (485:10-485:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (535:15-535:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (48:12-48:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (535:16-535:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (494:10-494:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (536:15-536:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (695:11-695:42)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (537:15-537:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (696:10-696:51)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (697:10-697:56)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:45)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (698:10-698:58)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:41)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (6:12-6:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (701:10-701:55)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (53:16-53:32)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (703:10-703:61)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (704:10-704:66)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (705:10-705:68)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:42)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (706:10-706:81)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (707:10-707:72)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (708:10-708:65)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:43)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (709:11-709:39)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (543:13-543:23)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (77:6-77:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (543:15-543:47)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (80:12-80:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (544:13-544:22)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (81:10-81:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (544:15-544:27)" [[concerns]] kind = "LintWarning" -document = "chanzuckerberg/czid-workflows:workflows/short-read-mngs/postprocess.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (82:10-82:36)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:23)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:data_structures/flag_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (124:10-124:29)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:26)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:data_structures/flag_filter.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (71:6-71:45)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:22)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (119:17-119:29)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:33)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (120:17-120:29)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:26)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (82:14-82:30)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (83:14-83:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:32)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/cellranger.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (87:14-87:25)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:33)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (141:11-141:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (142:11-142:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:31)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (151:12-151:18)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (54:16-54:34)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (152:12-152:18)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:31)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (168:14-168:30)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:32)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (169:15-169:31)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (73:11-73:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:31)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/fq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (74:11-74:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/kraken2.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (349:11-349:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:31)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/kraken2.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (350:11-350:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:25)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/librarian.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (30:11-30:21)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/md5sum.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (38:14-38:20)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:26)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/picard.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (119:15-119:39)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/picard.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (325:14-325:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:25)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/picard.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (420:14-420:28)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:40)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:tools/picard.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (481:14-481:29)" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:26)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (480:20-480:47)" +message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (481:19-481:41)" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (487:19-487:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:40)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (493:19-493:43)" +message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (499:19-499:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (505:19-505:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (511:30-511:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (512:28-512:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (513:27-513:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:46)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (514:24-514:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:21)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (515:24-515:48)" +message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (516:24-516:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (517:16-517:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (518:16-518:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:21)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (519:16-519:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (520:16-520:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (521:16-521:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (522:16-522:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (564:13-564:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (523:16-523:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (565:13-565:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (524:16-524:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (566:13-566:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (525:16-525:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (567:13-567:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (526:16-526:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (527:16-527:38)" +message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (528:16-528:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (529:16-529:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (530:16-530:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (531:16-531:35)" +message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:40)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (532:16-532:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (533:16-533:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (534:16-534:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (535:16-535:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (537:15-537:41)" +message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (538:15-538:45)" +message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:28)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (539:15-539:41)" +message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (540:15-540:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (541:15-541:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:28)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (542:15-542:43)" +message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (543:15-543:47)" +message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (544:15-544:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (545:13-545:23)" +message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:23)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (546:13-546:22)" +message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (547:13-547:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (548:13-548:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (549:13-549:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:23)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (550:13-550:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (551:13-551:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (552:13-552:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (553:13-553:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:44)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (554:13-554:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:46)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (555:13-555:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (556:13-556:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (557:13-557:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (558:13-558:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:33)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (559:13-559:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (55:16-55:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (560:13-560:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:33)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (561:13-561:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (562:13-562:21)" +message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (563:13-563:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:42)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (564:13-564:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (565:13-565:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:40)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (566:13-566:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (567:13-567:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:42)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (568:13-568:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (569:13-569:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:40)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (56:16-56:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:24)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (570:13-570:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (571:13-571:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (572:13-572:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (573:13-573:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:40)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (574:13-574:28)" +message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:44)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (575:13-575:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:24)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (576:13-576:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:26)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (577:13-577:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (578:13-578:23)" +message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:31)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (579:13-579:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (57:16-57:46)" +message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:26)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (580:13-580:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (581:13-581:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (582:13-582:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:25)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (583:13-583:33)" +message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (584:13-584:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (585:13-585:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:37)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (586:13-586:42)" +message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (587:13-587:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (588:13-588:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (589:13-589:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:37)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (58:16-58:40)" +message = "[v1::W006::Naming/Low] identifier must be snake case (598:13-598:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (590:13-590:24)" +message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (591:13-591:31)" +message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (592:13-592:26)" +message = "[v1::W006::Naming/Low] identifier must be snake case (59:16-59:44)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (593:13-593:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:35)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (594:13-594:25)" +message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (595:13-595:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:29)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (596:13-596:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (597:13-597:37)" +message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (598:13-598:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:35)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (599:13-599:34)" +message = "[v1::W006::Naming/Low] identifier must be snake case (603:13-603:36)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (59:16-59:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (604:13-604:27)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (600:13-600:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:13-60:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (601:13-601:29)" +message = "[v1::W006::Naming/Low] identifier must be snake case (60:16-60:44)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (602:13-602:35)" +message = "[v1::W006::Naming/Low] identifier must be snake case (61:13-61:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (603:13-603:36)" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:28)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (604:13-604:27)" +message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:30)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (60:16-60:44)" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:32)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (62:13-62:30)" +message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:34)" [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (63:13-63:32)" +message = "[v1::W006::Naming/Low] identifier must be snake case (64:13-64:25)" [[concerns]] kind = "LintWarning" @@ -55440,6 +58110,16 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (66:13-66:25)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (816:9-816:30)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/star.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (817:9-817:30)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" @@ -55455,16 +58135,36 @@ kind = "LintWarning" document = "stjudecloud/workflows:tools/star.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (820:9-820:30)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (24:17-24:23)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/util.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:23)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:tools/util.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (413:14-413:21)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:tools/util.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (415:14-415:21)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (49:21-49:27)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (50:22-50:28)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" @@ -55475,11 +58175,21 @@ kind = "LintWarning" document = "stjudecloud/workflows:workflows/general/bam-to-fastqs.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (52:22-52:28)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (570:11-570:35)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/qc/quality-check-standard.wdl" message = "[v1::W006::Naming/Low] identifier must be snake case (572:11-572:35)" +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (26:17-26:33)" + [[concerns]] kind = "LintWarning" document = "stjudecloud/workflows:workflows/reference/bwa-db-build.wdl" @@ -55487,93 +58197,103 @@ message = "[v1::W006::Naming/Low] identifier must be snake case (28:17-28:33)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (103:15-103:24)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (104:15-104:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:24)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (106:21-106:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (182:12-182:14)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (41:16-41:32)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (183:13-183:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (42:16-42:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (184:13-184:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (43:16-43:30)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (185:13-185:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:17-44:36)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (186:13-186:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:17-45:37)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (187:13-187:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (46:23-46:36)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (188:13-188:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (47:23-47:37)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (189:13-189:15)" +document = "stjudecloud/workflows:workflows/reference/gatk-reference.wdl" +message = "[v1::W007::Spacing/Low] missing newline at the end of the file (108:2-108:2)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (190:13-190:15)" +document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (125:14-125:21)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/reference/make-qc-reference.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (127:14-127:21)" + +[[concerns]] +kind = "LintWarning" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (33:17-33:33)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (191:10-191:12)" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (34:17-34:24)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (192:13-192:15)" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (35:17-35:33)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (193:13-193:15)" +document = "stjudecloud/workflows:workflows/reference/star-db-build.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (36:17-36:24)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (194:13-194:15)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (44:14-44:23)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (195:13-195:15)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl" +message = "[v1::W006::Naming/Low] identifier must be snake case (45:14-45:29)" [[concerns]] kind = "LintWarning" -document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-standard-fastq.wdl" -message = "[v1::W006::Naming/Low] identifier must be snake case (198:6-198:25)" +document = "stjudecloud/workflows:workflows/rnaseq/rnaseq-variant-calling.wdl" +message = "[v1::W007::Spacing/Low] multiple empty lines at the end of file (126:1-127:1)" [[concerns]] kind = "LintWarning"