Merge pull request #1283 from adamrtalbot/increase_coverage_of_defaul…

…t_test_snapshot Increase contents of default.main.nf.test.snap
nf-core · Apr 12, 2024 · d129b5a · d129b5a
2 parents 9e4cf57 + b903195
commit d129b5a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -65,6 +65,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1253](https://github.com/nf-core/rnaseq/pull/1253) - Use nf-test files as matrix to test over in CI/CD for efficiency
 - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
 - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
+- [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
 
 ### Parameters
 

diff --git a/tests/default.main.nf.test b/tests/default.main.nf.test
@@ -14,10 +14,27 @@ nextflow_pipeline {
         }
 
         then {
-            assert workflow.success
+
 
             assertAll(
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") }
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") },
+                { assert snapshot(
+                        path("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv"),
+                        path("${params.outdir}/custom/out/genome_gfp.fasta"),
+                        path("${params.outdir}/custom/out/genome_gfp.gtf"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"),
+                        path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig")
+                    ).match("output_files")
+                }
             )
         }
     }

diff --git a/tests/default.main.nf.test.snap b/tests/default.main.nf.test.snap
@@ -1,4 +1,26 @@
 {
+    "output_files": {
+        "content": [
+            "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17",
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
+            "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8",
+            "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e",
+            "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b",
+            "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737",
+            "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9",
+            "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466",
+            "WT_REP1.forward.bigWig:md5,92ad01ddd1dbb7f6d7e2eae23df58c7c",
+            "WT_REP1.reverse.bigWig:md5,dcac37ef5fff108afd0632388919dcf7",
+            "WT_REP2.forward.bigWig:md5,d10cbea27b82745b46077191d3ff2820",
+            "WT_REP2.reverse.bigWig:md5,2b3a15b511efdbc838574200ee2bec0c"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-11T14:39:58.637279952"
+    },
     "software_versions": {
         "content": [
             "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.19.2}, SAMTOOLS_IDXSTATS={samtools=1.19.2}, SAMTOOLS_INDEX={samtools=1.19.2}, SAMTOOLS_SORT={samtools=1.19.2}, SAMTOOLS_STATS={samtools=1.19.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"