feat: addition of vembrane sort module #9294
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mkatsanto
moved this from To do
to Ready for review
in Hackathon Barcelona October 2025
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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| { assert snapshot(process.out).match() } | |
| { assert snapshot( | |
| process.out, | |
| path(process.out.versions[0]).yaml | |
| ).match() } |
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This is added in the other PR right?, can you remove it here? :)
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Sorry, what I meant: can you please do one PR per module :) meaning one seperate one for vembrane/table?
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Can you run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment modules/nf-core/vembrane/sort/main.nf
please? :)
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Seems like gzipped vcfs are not allowed. I would suggest to open an issue over at the vembrane repo to request that and remove it from the module for now :) You can link to the PR in the issue you open :) |
| test("homo_sapiens - [vcf] - vcf - compressed_output") { | ||
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| config "./nextflow.config" | ||
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| when { | ||
| params { | ||
| vembrane_args = '--output-fmt vcf.gz' | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_gz' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) | ||
| ] | ||
| input[1] = 'QUAL' | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } |
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| test("homo_sapiens - [vcf] - vcf - compressed_output") { | |
| config "./nextflow.config" | |
| when { | |
| params { | |
| vembrane_args = '--output-fmt vcf.gz' | |
| } | |
| process { | |
| """ | |
| input[0] = [ | |
| [ id:'test_gz' ], // meta map | |
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) | |
| ] | |
| input[1] = 'QUAL' | |
| """ | |
| } | |
| } | |
| then { | |
| assertAll( | |
| { assert process.success }, | |
| { assert snapshot(process.out).match() } | |
| ) | |
| } | |
| } |
| - "*.vcf*": | ||
| type: file | ||
| description: Sorted VCF file (can be compressed) | ||
| pattern: "*.{vcf,vcf.gz}" |
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| pattern: "*.{vcf,vcf.gz}" | |
| pattern: "*.{vcf,bcf}" |
| val expression | ||
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| output: | ||
| tuple val(meta), path("*.vcf*"), emit: vcf |
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| tuple val(meta), path("*.vcf*"), emit: vcf | |
| tuple val(meta), path("*.{vcf.gz,vcf,bcf}"), emit: vcf |
| def suffix = args.contains('--output-fmt vcf.gz') | ||
| ? 'vcf.gz' |
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I thought this is failing 🤔
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@mkatsanto do you have time to finish this? :) then I would give it another round of review - or do you need some help / me to pick it up (both would be fine!) |
@famosab I can do this tomorrow, but if you are in a hurry please go ahead! |
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No, no hurry at all :) I was just wondering because we never talked about it during the Hackathon! Thank you!!! |
3 participants
PR checklist
Fixes #9265
Addition of the vembrane sort module https://github.com/vembrane/vembrane
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda