Vembrane filter #9290
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Vembrane filter #9290
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trangdo-hsc
moved this from To do
to Ready for review
in Hackathon Barcelona October 2025
famosab
reviewed
Oct 29, 2025
famosab
reviewed
Oct 29, 2025
famosab
requested changes
Oct 29, 2025
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| // | ||
| // (the module requires running more than one process to generate the required output) | ||
| // add the 'setup' method here. | ||
| // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). | ||
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| // | |
| // (the module requires running more than one process to generate the required output) | |
| // add the 'setup' method here. | |
| // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). |
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map |
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| [ id:'test', single_end:false ], // meta map | |
| [ id:'test' ], // meta map |
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map |
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| [ id:'test', single_end:false ], // meta map | |
| [ id:'test' ], // meta map |
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map |
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| [ id:'test', single_end:false ], // meta map | |
| [ id:'test' ], // meta map |
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map |
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| [ id:'test', single_end:false ], // meta map | |
| [ id:'test' ], // meta map |
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| tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: filtered_variant | ||
| path "versions.yml", emit: versions |
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Can you align the emit statements? (I know that this was destroyed by the linter but it looks better in the end :D)
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| vembrane filter \\ | ||
| ${args} \\ | ||
| ${expression} \\ | ||
| -o ${prefix}_filtered.vcf \\ | ||
| ${variant} |
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For the stub we actually want to create "fake files" that resemble whatever we produce in the script block
| e.g. [ id:'test', single_end:false ] | ||
| - "*.{vcf,bcf,vcf.gz,bcf.gz}": | ||
| type: file | ||
| description: VCF normalized output file |
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda