first pass test updates

bactopia · Mar 23, 2024 · 485a78f · 485a78f
1 parent 92e97b9
commit 485a78f
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Showing 15 changed files with 41 additions and 41 deletions.
diff --git a/subworkflows/local/assembler/test.yml b/subworkflows/local/assembler/test.yml
@@ -46,7 +46,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill-se.log
       contains: ['skesa', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 3e25df3e4019a1ef305a2c110d12ac9e
+      md5sum: ca2bf722c9d05b082a101c3e13068dd6
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -100,7 +100,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill-se.log
       contains: ['spades', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 3e25df3e4019a1ef305a2c110d12ac9e
+      md5sum: ca2bf722c9d05b082a101c3e13068dd6
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -141,7 +141,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill-se.log
       contains: ['megahit', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 3e25df3e4019a1ef305a2c110d12ac9e
+      md5sum: ca2bf722c9d05b082a101c3e13068dd6
     - path: bactopia/portiera/main/assembler/megahit-unpolished.gfa.gz
     - path: bactopia/portiera/main/assembler/portiera-assembly-error.txt
       md5sum: 173bfef2b0d5bd31c1b76cb37de67d3c
@@ -196,7 +196,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill-se.log
       contains: ['velvet', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 3e25df3e4019a1ef305a2c110d12ac9e
+      md5sum: ca2bf722c9d05b082a101c3e13068dd6
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -253,7 +253,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill.log
       contains: ['skesa', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: e16c349ed6815e53930f7ffe6a7bfe31
+      md5sum: 377dba6d337bec8d81da248be05badff
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -311,7 +311,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill.log
       contains: ['spades', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: e16c349ed6815e53930f7ffe6a7bfe31
+      md5sum: 377dba6d337bec8d81da248be05badff
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -356,7 +356,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill.log
       contains: ['megahit', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: e16c349ed6815e53930f7ffe6a7bfe31
+      md5sum: 377dba6d337bec8d81da248be05badff
     - path: bactopia/portiera/main/assembler/megahit-unpolished.gfa.gz
     - path: bactopia/portiera/main/assembler/portiera-assembly-error.txt
       md5sum: 173bfef2b0d5bd31c1b76cb37de67d3c
@@ -415,7 +415,7 @@
     - path: bactopia/portiera/main/assembler/logs/shovill.log
       contains: ['velvet', 'shovill', 'Done']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: e16c349ed6815e53930f7ffe6a7bfe31
+      md5sum: 377dba6d337bec8d81da248be05badff
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -468,7 +468,7 @@
     - path: bactopia/portiera/main/assembler/logs/unicycler.log
       contains: ['unicycler', 'complete', 'Saving']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 2e6bd6eec63b11939965e16fac507047
+      md5sum: 227506881d670f1977dc013695de8042
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -526,7 +526,7 @@
     - path: bactopia/portiera/main/assembler/logs/nf-assembler.trace
       contains: ['nextflow.trace']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 48ef4021a79c8b84dc914daf54658724
+      md5sum: 543bba4536419bd2950e63af41eb048c
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -578,7 +578,7 @@
     - path: bactopia/portiera/main/assembler/logs/nf-assembler.trace
       contains: ['nextflow.trace']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 48ef4021a79c8b84dc914daf54658724
+      md5sum: 543bba4536419bd2950e63af41eb048c
     - path: bactopia/portiera/main/assembler/miniasm-unpolished.fasta.gz
     - path: bactopia/portiera/main/assembler/miniasm-unpolished.gfa.gz
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
@@ -632,7 +632,7 @@
     - path: bactopia/portiera/main/assembler/logs/nf-assembler.trace
       contains: ['nextflow.trace']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 48ef4021a79c8b84dc914daf54658724
+      md5sum: 543bba4536419bd2950e63af41eb048c
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
@@ -689,7 +689,7 @@
     - path: bactopia/portiera/main/assembler/logs/nf-assembler.trace
       contains: ['nextflow.trace']
     - path: bactopia/portiera/main/assembler/logs/versions.yml
-      md5sum: 1d314cef9ccaeaa0a89323441a0cdf4b
+      md5sum: 518e7c708c9f142e5da2c2d05feb858e
     - path: bactopia/portiera/main/assembler/portiera.fna.gz
     - path: bactopia/portiera/main/assembler/portiera.tsv
       contains: ["total_contig"]
diff --git a/subworkflows/local/blastn/test.yml b/subworkflows/local/blastn/test.yml
@@ -41,7 +41,7 @@
     - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
-      md5sum: 05f4d83f9689ca445c89d2c14286042e
+      md5sum: e7b15a1f93b7936b51f64d5f8cfa1430
 
 - name: blastn-test_gz
   command: bash -c 'nextflow run ./subworkflows/local/blastn/test.nf -entry test_blastn_gz --wf blastn -c nextflow.config ${BACTOPIA_ARGS}'
@@ -86,7 +86,7 @@
     - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
-      md5sum: 265c014c7328186a307cb9430da090af
+      md5sum: 3467e2150f3731b6d4af94bbdc821435
 
 - name: blastn-test_use_genes
   command: bash -c 'nextflow run ./subworkflows/local/blastn/test.nf -entry test_blastn_use_genes --wf blastn -c nextflow.config ${BACTOPIA_ARGS}'
@@ -131,4 +131,4 @@
     - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
-      md5sum: 0ff2ad9ce7ba1cc1fad83f8d59143d95
+      md5sum: 9a2a043009edd887f1c9b030639ad297
diff --git a/subworkflows/local/blastp/test.yml b/subworkflows/local/blastp/test.yml
@@ -41,7 +41,7 @@
     - path: bactopia/SRX1390622/tools/blastp/logs/nf-blastp.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastp/logs/versions.yml
-      md5sum: 42af37b58f6cc9837dda5793201993ad
+      md5sum: 9f491f4e6eb74583235d93a8602bdc18
 
 - name: blastp-test_gz
   command: bash -c 'nextflow run ./subworkflows/local/blastp/test.nf -entry test_blastp_gz --wf blastp -c nextflow.config ${BACTOPIA_ARGS}'
@@ -86,4 +86,4 @@
     - path: bactopia/SRX1390622/tools/blastp/logs/nf-blastp.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastp/logs/versions.yml
-      md5sum: e05afd6a41f0da42f1986bc55cc3be16
+      md5sum: d112a07590e131823d0c9c58d6c5b9d1
diff --git a/subworkflows/local/blastx/test.yml b/subworkflows/local/blastx/test.yml
@@ -41,7 +41,7 @@
     - path: bactopia/SRX1390622/tools/blastx/logs/nf-blastx.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastx/logs/versions.yml
-      md5sum: 88d3f94ad239f30a3111453a0820ded0
+      md5sum: 30cd58a6281aabb883e2aab6921cbb8a
 
 - name: blastx-test_gz
   command: bash -c 'nextflow run ./subworkflows/local/blastx/test.nf -entry test_blastx_gz --wf blastx -c nextflow.config ${BACTOPIA_ARGS}'
@@ -86,7 +86,7 @@
     - path: bactopia/SRX1390622/tools/blastx/logs/nf-blastx.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastx/logs/versions.yml
-      md5sum: 81018f9cceaba2644c3d39ee54fd0762
+      md5sum: 15d04184c55d7d1e3e06082de6add346
 
 - name: blastx-test_use_genes
   command: bash -c 'nextflow run ./subworkflows/local/blastx/test.nf -entry test_blastx_use_genes --wf blastx -c nextflow.config ${BACTOPIA_ARGS}'
@@ -131,4 +131,4 @@
     - path: bactopia/SRX1390622/tools/blastx/logs/nf-blastx.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/blastx/logs/versions.yml
-      md5sum: cfa85183171f3cca6e72a95b81f9aee8
+      md5sum: 83ce699112b9925c193160e5268c9e83
diff --git a/subworkflows/local/bracken/test.yml b/subworkflows/local/bracken/test.yml
@@ -43,7 +43,7 @@
     - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRR2838702/tools/bracken/logs/versions.yml
-      md5sum: 9bc7a68e6fd16c2dfe5f6eb0d687439f
+      md5sum: 3664924a9120258ea44d3858e1b0414f
 
 - name: bracken-test-tarball
   command: bash -c 'nextflow run ./subworkflows/local/bracken/test.nf -entry test_bracken_tarball --wf bracken -c nextflow.config ${BACTOPIA_ARGS}'
@@ -91,4 +91,4 @@
     - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRR2838702/tools/bracken/logs/versions.yml
-      md5sum: dafd32420071ec6ea5b9df4866c5c7c0
+      md5sum: 02436c5ee78bd3e7624fa2cebfa1af6b
diff --git a/subworkflows/local/genotyphi/test.yml b/subworkflows/local/genotyphi/test.yml
@@ -20,7 +20,7 @@
     - path: bactopia/bactopia-runs/genotyphi/merged-results/logs/genotyphi-concat/versions.yml
       contains: ['csvtk']
     - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-dag.dot
-      md5sum: 1b407e59487039bdbe295275cb4aef72
+      contains: ['genotyphi', 'GENOTYPHI', 'versions']
     - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-report.html
       contains: ['html', 'Nextflow', 'Report']
     - path: bactopia/bactopia-runs/genotyphi/nf-reports/genotyphi-timeline.html
@@ -54,7 +54,7 @@
     - path: bactopia/test/tools/genotyphi/logs/mykrobe/nf-genotyphi.trace
       contains: ['nextflow.trace']
     - path: bactopia/test/tools/genotyphi/logs/mykrobe/versions.yml
-      md5sum: 82aff618ee15aa872566d48a3c527437
+      md5sum: 38bcd32a145fbf05894aa0bfcfe66c05
     - path: bactopia/test/tools/genotyphi/test.csv
       contains: ["susceptibility", "typhi", "variants"]
     - path: bactopia/test/tools/genotyphi/test.json

diff --git a/subworkflows/local/kraken2/test.yml b/subworkflows/local/kraken2/test.yml
@@ -32,7 +32,7 @@
     - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRR2838702/tools/kraken2/logs/versions.yml
-      md5sum: 95cd3bacf8fa7d6f24cd6a539966ee3f
+      md5sum: 1bf6c7edd3b3090ae68f75f6db354736
 
 - name: kraken2-test-tarball
   command: bash -c 'nextflow run ./subworkflows/local/kraken2/test.nf -entry test_kraken2_tarball --wf kraken2 -c nextflow.config ${BACTOPIA_ARGS}'
@@ -69,4 +69,4 @@
     - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRR2838702/tools/kraken2/logs/versions.yml
-      md5sum: a61f15dab97c2fb0374fc6156e0f446b
+      md5sum: f6e71f7db9aa79ff598b29485f2496d0
diff --git a/subworkflows/local/mashtree/test.yml b/subworkflows/local/mashtree/test.yml
@@ -19,7 +19,7 @@
     - path: bactopia/bactopia-runs/mashtree/mashtree/logs/nf-mashtree.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/mashtree/mashtree/logs/versions.yml
-      md5sum: 96538caf6e99cea2c6efe23f3b70bd9f
+      md5sum: 46f17a27efed26210ef70f8e835fbfc5
     - path: bactopia/bactopia-runs/mashtree/mashtree/mashtree.dnd
       contains: ['GCF_000009885', 'GCF_000017085']
     - path: bactopia/bactopia-runs/mashtree/mashtree/mashtree.tsv

diff --git a/subworkflows/local/mobsuite/test.yml b/subworkflows/local/mobsuite/test.yml
@@ -47,6 +47,6 @@
     - path: bactopia/GCF_000017085/tools/mobsuite/logs/nf-mobsuite.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCF_000017085/tools/mobsuite/logs/versions.yml
-      md5sum: 70b7c16bd3f101f8ccf96a5640b7e2f8
+      md5sum: 4f2f3c349d4e30d595aeb67fc4934afd
     - path: bactopia/GCF_000017085/tools/mobsuite/plasmid_AA840.fasta
       md5sum: f774ed2069f1dfacd930673b748faaac
diff --git a/subworkflows/local/mykrobe/test.yml b/subworkflows/local/mykrobe/test.yml
@@ -42,7 +42,7 @@
     - path: bactopia/test/tools/mykrobe/logs/nf-mykrobe.trace
       contains: ['nextflow.trace']
     - path: bactopia/test/tools/mykrobe/logs/versions.yml
-      md5sum: 9b226e8dcf0cbd7a9055291126babfd0
+      md5sum: cb986756df70555ad35b1644d1bd403c
     - path: bactopia/test/tools/mykrobe/test.csv
       contains: ["susceptibility", "staph", "variants"]
     - path: bactopia/test/tools/mykrobe/test.json

diff --git a/subworkflows/local/rgi/test.yml b/subworkflows/local/rgi/test.yml
@@ -31,7 +31,7 @@
     - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/nf-merged-results.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/rgi/merged-results/logs/rgi-heatmap/versions.yml
-      md5sum: c16a8469ca85a97204a631a52190323d
+      md5sum: 47dd197ef74cfe2af440ddf5b6a56c72
     - path: bactopia/bactopia-runs/rgi/merged-results/rgi-2.csv
       contains: ["gene", "Klebsiella", "Escherichia"]
     - path: bactopia/bactopia-runs/rgi/merged-results/rgi-2.eps
@@ -64,7 +64,7 @@
     - path: bactopia/GCA_000027305/tools/rgi/logs/nf-rgi.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCA_000027305/tools/rgi/logs/versions.yml
-      md5sum: 81482750f2ba727c718e24bf844293e8
+      md5sum: 8a5ec5372a0936c4f30740344b771701
     - path: bactopia/GCF_900478275/tools/rgi/GCF_900478275.json
       contains: ["type_match", "model_name", "orf_dna_sequence"]
     - path: bactopia/GCF_900478275/tools/rgi/GCF_900478275.txt
@@ -82,4 +82,4 @@
     - path: bactopia/GCF_900478275/tools/rgi/logs/nf-rgi.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCF_900478275/tools/rgi/logs/versions.yml
-      md5sum: 81482750f2ba727c718e24bf844293e8
+      md5sum: 8a5ec5372a0936c4f30740344b771701
diff --git a/subworkflows/local/seroba/test.yml b/subworkflows/local/seroba/test.yml
@@ -20,7 +20,7 @@
     - path: bactopia/bactopia-runs/seroba/merged-results/seroba.tsv
       md5sum: b3983df1ed608ca335bfcb66b22b8b94
     - path: bactopia/bactopia-runs/seroba/nf-reports/seroba-dag.dot
-      md5sum: a59071f842746266f80ab67bb3a06aa7
+      contains: ['serobadag', 'SEROBA', 'versions']
     - path: bactopia/bactopia-runs/seroba/nf-reports/seroba-report.html
       contains: ['html', 'Nextflow', 'Report']
     - path: bactopia/bactopia-runs/seroba/nf-reports/seroba-timeline.html

diff --git a/subworkflows/local/tblastn/test.yml b/subworkflows/local/tblastn/test.yml
@@ -41,7 +41,7 @@
     - path: bactopia/SRX1390622/tools/tblastn/logs/nf-tblastn.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/tblastn/logs/versions.yml
-      md5sum: c6c83cf9a0ca3a400c923feca9b88d07
+      md5sum: 531f2b629a61a8bb25f6bdc9f1e15d14
 
 - name: tblastn-test_gz
   command: bash -c 'nextflow run ./subworkflows/local/tblastn/test.nf -entry test_tblastn_gz --wf tblastn -c nextflow.config ${BACTOPIA_ARGS}'
@@ -86,4 +86,4 @@
     - path: bactopia/SRX1390622/tools/tblastn/logs/nf-tblastn.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/tblastn/logs/versions.yml
-      md5sum: bbf653d96871a63433b5e848fba069fc
+      md5sum: c2b46d805e7b1f0f1597884b57a7a3e8
diff --git a/subworkflows/local/tblastx/test.yml b/subworkflows/local/tblastx/test.yml
@@ -41,7 +41,7 @@
     - path: bactopia/SRX1390622/tools/tblastx/logs/nf-tblastx.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/tblastx/logs/versions.yml
-      md5sum: 120c6925adb5648d8cbbc7580a8f2973
+      md5sum: 437af4df6d319abf59d1f04fb89ceb97
 
 - name: tblastx-test_gz
   command: bash -c 'nextflow run ./subworkflows/local/tblastx/test.nf -entry test_tblastx_gz --wf tblastx -c nextflow.config ${BACTOPIA_ARGS}'
@@ -86,4 +86,4 @@
     - path: bactopia/SRX1390622/tools/tblastx/logs/nf-tblastx.trace
       contains: ['nextflow.trace']
     - path: bactopia/SRX1390622/tools/tblastx/logs/versions.yml
-      md5sum: 18a4801a563bfac01aa252fae6e608b7
+      md5sum: 29318e469b9018d56b2af2636dc954c5
diff --git a/subworkflows/local/tbprofiler/test.yml b/subworkflows/local/tbprofiler/test.yml
@@ -28,11 +28,11 @@
     - path: bactopia/test/tools/tbprofiler/logs/nf-tbprofiler.trace
       contains: ['nextflow.trace']
     - path: bactopia/test/tools/tbprofiler/logs/versions.yml
-      md5sum: 1395cb7dfca1a1a6afce11e0178c905c
+      md5sum: f325188a7b7cb206a4212a71119b6ae7
     - path: bactopia/test/tools/tbprofiler/test.results.csv
-      contains: ['gid', 'Analysis', 'freebayes']
+      contains: ['gid', 'Analysis']
     - path: bactopia/test/tools/tbprofiler/test.results.json
       contains: ['locus_tag', 'tbprofiler_version', 'median_depth']
     - path: bactopia/test/tools/tbprofiler/test.results.txt
-      contains: ['gid', 'Analysis', 'freebayes']
+      contains: ['gid', 'Analysis']
     - path: bactopia/test/tools/tbprofiler/vcf/test.targets.csq.vcf.gz