Remove the usage of parameters in subworkflows#753
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ramprasadn merged 13 commits intodevfrom Dec 10, 2025
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@nf-core-bot fix linting |
fellen31
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Dec 5, 2025
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fellen31
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Nice! Some questions about the tests.
| skip_peddy, | ||
| skip_qualimap, | ||
| skip_smncopynumbercaller, | ||
| skip_vcf2cytosure |
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| skip_vcf2cytosure | |
| skip_vcf2cytosure, |
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Think nextflow lint -f might add commas here, but not sure.
| skip_tools = null | ||
| platform = "illumina" | ||
| min_trimmed_length = 50 | ||
| mito_name = "MT" |
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In the config for the test.
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| workflow.out.mt_bam_bai | ||
| .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, | ||
| workflow.out.mt_bam_bai_gatksubwf | ||
| .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, | ||
| workflow.out.mtshift_bam_bai_gatksubwf | ||
| .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, |
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I wouldn't mind seeing that these are empty.
| params { | ||
| mt_aligner = 'bwa' | ||
| outdir = "$outputDir" | ||
| outdir = "$outputDir" |
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Why do you need outdir here? 🤔
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We don't need it for the tests to work, but nf-test throws a warning in verbose mode when its not set.
| when { | ||
| params { | ||
| aligner = "sentieon" | ||
| outdir = "$outputDir" |
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Don't understand why outdir is needed?
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| "HAPLOGREP3_CLASSIFY_MT": { | ||
| "haplogrep3": null | ||
| }, |
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Good catch! I am updating the module nf-core/modules#9523
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| "REPLACE_SPACES_IN_VCFINFO": { | ||
| "replace_spaces_in_vcfinfo": "v1.0", | ||
| "python": "3.8.3" | ||
| }, |
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Why are so many more files output? Is this PR supposed to change the tests?
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Yes! We are not skipping as many tests like we used to.
| "-profile test_bam": { | ||
| "content": [ | ||
| 274, | ||
| 794, |
| "-profile test_singleton": { | ||
| "content": [ | ||
| 148, | ||
| 362, |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).