-
Notifications
You must be signed in to change notification settings - Fork 10
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Refactor tests #152
Merged
Merged
Refactor tests #152
Changes from all commits
Commits
Show all changes
7 commits
Select commit
Hold shift + click to select a range
e5037b7
build: Add nft-bam
edmundmiller 4297d9c
build: Bump nft-bam version
edmundmiller f3f3070
test: Write first bam test
edmundmiller b9d0394
test: Refactor default test
edmundmiller 5e9a6c1
test: Refactor all the tests
edmundmiller 8b6cfc6
test: Use small_samplesheet
edmundmiller 04d4162
test: Fix non-deterministic tests
edmundmiller File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| sample,fastq_1,fastq_2 | ||
| cd4_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T1.fastq.gz, | ||
| cd4_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz, | ||
| jurkat,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882904_T1.fastq.gz, |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| // Function to remove Nextflow version from pipeline_software_mqc_versions.yml | ||
|
|
||
| class UTILS { | ||
| public static String removeNextflowVersion(pipeline_software_mqc_versions) { | ||
| def softwareVersions = path(pipeline_software_mqc_versions).yaml | ||
| if (softwareVersions.containsKey("Workflow")) { | ||
| softwareVersions.Workflow.remove("Nextflow") | ||
| } | ||
| return softwareVersions | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| nextflow_pipeline { | ||
|
|
||
| name "Bowtie2" | ||
| script "../../../main.nf" | ||
| tag "aligner" | ||
| tag "bowtie2" | ||
|
|
||
| test("Should run with defaults") { | ||
|
|
||
| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| aligner = "bowtie2" | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") }, | ||
| { assert snapshot( | ||
| workflow.trace.tasks().size(), | ||
| path("$outputDir/bbmap").list(), | ||
| // BUG https://github.com/nf-core/nascent/issues/102 | ||
| // path("$outputDir/bedtools").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/gene").list(), | ||
| // FIXME cd4 isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/predicted").list(), | ||
| // path("$outputDir/deeptools").list(), | ||
| // path("$outputDir/fastp/*.json").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/gtf2bed").list(), | ||
| path("$outputDir/homer/cd4.bed"), | ||
| path("$outputDir/homer/jurkat.bed"), | ||
| // FIXME https://github.com/nf-core/nascent/issues/148 | ||
| // path("$outputDir/preseq").list(), | ||
| // path("$outputDir/rseqc").list(), | ||
| // FIXME Bowtie2 isn't deterministic | ||
| bam("$outputDir/samtools/cd4_REP1.sorted.bam").getHeaderMD5(), | ||
| bam("$outputDir/samtools/cd4_REP2.sorted.bam").getHeaderMD5(), | ||
| bam("$outputDir/samtools/jurkat.sorted.bam").getHeaderMD5(), | ||
| ).match("output_files") | ||
| } | ||
| ) | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| { | ||
| "output_files": { | ||
| "content": [ | ||
| 75, | ||
| [ | ||
| "cd4_REP1.coverage.hist.txt:md5,ffd8c0a94869dd782779fc871a9b781a", | ||
| "cd4_REP1.coverage.stats.txt:md5,bebdef1adcce4296878f8699a0f5cb32", | ||
| "cd4_REP2.coverage.hist.txt:md5,6e0ca13df7b06ff6a81fb21596df4ca4", | ||
| "cd4_REP2.coverage.stats.txt:md5,ffb701c2be33360a96ce85b1330b13f8", | ||
| "jurkat.coverage.hist.txt:md5,656e30e8c4bd12e45a036c62c18730c1", | ||
| "jurkat.coverage.stats.txt:md5,627f0ec96ea9bdbd7f41b09b64c389d6" | ||
| ], | ||
| "cd4.bed:md5,c311e32ebdca7f3e978a271407de7241", | ||
| "jurkat.bed:md5,5e170e72c4e2b27a7bb0a6de7b735c1c", | ||
| "7945f971cd63ad99ff2d9cc81e19ea39", | ||
| "43982cec9077e7030428267841cf04ef", | ||
| "8813c6dd42cabd94042f4f9e4aee3560" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T22:17:27.92555495" | ||
| }, | ||
| "software_versions": { | ||
| "content": [ | ||
| "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BOWTIE2_ALIGN={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T21:20:15.261777672" | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| nextflow_pipeline { | ||
|
|
||
| name "BWA" | ||
| script "../../../main.nf" | ||
| tag "aligner" | ||
| tag "bwa" | ||
|
|
||
| test("Should run with defaults") { | ||
|
|
||
| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| aligner = "bwa" | ||
| input = "${projectDir}/assets/samplesheet.csv" | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") }, | ||
| { assert snapshot( | ||
| workflow.trace.tasks().size(), | ||
| path("$outputDir/bbmap").list(), | ||
| // BUG https://github.com/nf-core/nascent/issues/102 | ||
| // path("$outputDir/bedtools").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/gene").list(), | ||
| // FIXME cd4 isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/predicted").list(), | ||
| // path("$outputDir/deeptools").list(), | ||
| // path("$outputDir/fastp/*.json").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/gtf2bed").list(), | ||
| path("$outputDir/homer/cd4.bed"), | ||
| path("$outputDir/homer/jurkat.bed"), | ||
| // FIXME https://github.com/nf-core/nascent/issues/148 | ||
| // path("$outputDir/preseq").list(), | ||
| // path("$outputDir/rseqc").list(), | ||
| bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/cd4_REP3.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/cd4_REP4.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/jurkat_REP1.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/jurkat_REP2.sorted.bam").getSamLinesMD5(), | ||
| ).match("output_files") | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| def igenomes_base = 's3://ngi-igenomes/igenomes' | ||
|
|
||
| // https://github.com/nf-core/nascent/issues/106 | ||
| test("Should work with BWA Index") { | ||
| // FIXME PINTS Fails because it doesn't find anything. | ||
| config '../skip_pints.config' | ||
| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| aligner = "bwa" | ||
| // TODO Update these to human | ||
| bwa_index = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" | ||
| fasta = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" | ||
| gtf = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assert workflow.success | ||
| assert snapshot( | ||
| workflow.trace.tasks().size(), | ||
| ).match() | ||
| } | ||
| } | ||
|
|
||
| // https://github.com/nf-core/nascent/issues/119 | ||
| test("Should work with gzipped references") { | ||
| config '../skip_gzip.config' | ||
| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| aligner = "bwa" | ||
| fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta.gz' | ||
| gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz' | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assert workflow.success | ||
| assert snapshot( | ||
| workflow.trace.tasks().size(), | ||
| ).match() | ||
| } | ||
|
|
||
| } | ||
| } | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| { | ||
| "output_files": { | ||
| "content": [ | ||
| 134, | ||
| [ | ||
| "cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2", | ||
| "cd4_REP1.coverage.stats.txt:md5,f1471b61ac17dba283d80e08450c7e55", | ||
| "cd4_REP2.coverage.hist.txt:md5,8d5258a0882494bc4e3f1aa6aa5ed685", | ||
| "cd4_REP2.coverage.stats.txt:md5,3cdb4473211f9da44166ffa6aaa5b602", | ||
| "cd4_REP3.coverage.hist.txt:md5,4a8397c1ea08f35ca7046e3c2c014a08", | ||
| "cd4_REP3.coverage.stats.txt:md5,b88592b469d504a93f2389255ac15f38", | ||
| "cd4_REP4.coverage.hist.txt:md5,d2cbf89e1f753d99bcd03b4e472270dd", | ||
| "cd4_REP4.coverage.stats.txt:md5,4c2b5fe6793aab8560cc87c176ac06ab", | ||
| "jurkat_REP1.coverage.hist.txt:md5,71a893d9d1d55fd47399f6d47b628d6e", | ||
| "jurkat_REP1.coverage.stats.txt:md5,381c69a30099d82066a959deab1a2569", | ||
| "jurkat_REP2.coverage.hist.txt:md5,d124bdadaf2dc5cdd9e3db5a1ab4c588", | ||
| "jurkat_REP2.coverage.stats.txt:md5,b1940346719e4070091f2eef6e508f49" | ||
| ], | ||
| "cd4.bed:md5,ab94918610a560772fdbec591200295f", | ||
| "jurkat.bed:md5,41908723fa423a78476feb2e7627a3a4", | ||
| "c529a16c839e85e119b98354f109352d", | ||
| "9e63b682af88fa902cf92b5c485845b1", | ||
| "2aa200bbbce374ec7dedb9b46ce4aae1", | ||
| "122274730dd5386e1b26c174df886a8b", | ||
| "c2adf5327ff6d4edda2fdad00c7cb9bf", | ||
| "63fea3b1e2e08e5f6fdf3f7ba0aa7818" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T08:58:17.037588077" | ||
| }, | ||
| "Should work with gzipped references": { | ||
| "content": [ | ||
| 53 | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T07:39:38.160960801" | ||
| }, | ||
| "software_versions": { | ||
| "content": [ | ||
| "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWA_MEM={bwa=0.7.18-r1243-dirty, samtools=1.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T07:37:00.256122533" | ||
| }, | ||
| "Should work with BWA Index": { | ||
| "content": [ | ||
| 59 | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T07:38:19.100788775" | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| nextflow_pipeline { | ||
|
|
||
| name "bwamem2" | ||
| script "../../../main.nf" | ||
|
|
||
| test("Should run with defaults") { | ||
|
|
||
| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| aligner = "bwamem2" | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") }, | ||
| { assert snapshot( | ||
| workflow.trace.tasks().size(), | ||
| path("$outputDir/bbmap").list(), | ||
| // BUG https://github.com/nf-core/nascent/issues/102 | ||
| // path("$outputDir/bedtools").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/gene").list(), | ||
| // FIXME cd4 isn't deterministic | ||
| // path("$outputDir/bwa/featurecounts/predicted").list(), | ||
| // path("$outputDir/deeptools").list(), | ||
| // path("$outputDir/fastp/*.json").list(), | ||
| // FIXME gtf2bed isn't deterministic | ||
| // path("$outputDir/gtf2bed").list(), | ||
| path("$outputDir/homer/cd4.bed"), | ||
| path("$outputDir/homer/jurkat.bed"), | ||
| // FIXME https://github.com/nf-core/nascent/issues/148 | ||
| // path("$outputDir/preseq").list(), | ||
| // path("$outputDir/rseqc").list(), | ||
| bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(), | ||
| bam("$outputDir/samtools/jurkat.sorted.bam").getSamLinesMD5(), | ||
| ).match("output_files") | ||
| } | ||
| ) | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| { | ||
| "output_files": { | ||
| "content": [ | ||
| 77, | ||
| [ | ||
| "cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2", | ||
| "cd4_REP1.coverage.stats.txt:md5,f1471b61ac17dba283d80e08450c7e55", | ||
| "cd4_REP2.coverage.hist.txt:md5,8d5258a0882494bc4e3f1aa6aa5ed685", | ||
| "cd4_REP2.coverage.stats.txt:md5,3cdb4473211f9da44166ffa6aaa5b602", | ||
| "jurkat.coverage.hist.txt:md5,71a893d9d1d55fd47399f6d47b628d6e", | ||
| "jurkat.coverage.stats.txt:md5,381c69a30099d82066a959deab1a2569" | ||
| ], | ||
| "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062", | ||
| "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb", | ||
| "c529a16c839e85e119b98354f109352d", | ||
| "9e63b682af88fa902cf92b5c485845b1", | ||
| "c2adf5327ff6d4edda2fdad00c7cb9bf" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-03T10:28:23.205786296" | ||
| }, | ||
| "software_versions": { | ||
| "content": [ | ||
| "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWAMEM2_MEM={bwamem2=2.2.1, samtools=1.19.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}" | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-01T19:59:55.332896924" | ||
| } | ||
| } |
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I guess this is intentionally left with comments, isn't it?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yeah, I hadn't figured out the test flaking out. I also have a PR coming up to refactor the outputs as well, so it's a bit of a waste to try to get the tests working when it's all getting reworked.