pypgx/createinputvcf #6720
pypgx/createinputvcf #6720
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Jorisvansteenbrugge
requested review from
koenbossers
and removed request for
a team
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def assembly = task.ext.assembly_version ?: "GRCh38" |
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This should be a value input. We don't allow additional external arguments to keep everything consistent
| def args = task.ext.args ?: '' | ||
| def assembly = task.ext.assembly_version ?: "GRCh38" | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def pgx_genes = "--genes ${task.ext.pgx_genes.join(' ')}" ?: '' |
| ${args} \\ | ||
| ${pgx_genes} \\ | ||
| --assembly ${assembly} \\ | ||
| ${prefix}_variants.vcf.gz \\ |
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| ${prefix}_variants.vcf.gz \\ | |
| ${prefix}.vcf.gz \\ |
This is to maintain the flexibility of prefix you can add _variants there if you want to add this to the file name
| touch ${prefix}_variants.vcf.gz | ||
| touch ${prefix}_variants.vcf.gz.tbi |
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| touch ${prefix}_variants.vcf.gz | |
| touch ${prefix}_variants.vcf.gz.tbi | |
| echo "" | gzip > ${prefix}.vcf.gz | |
| touch ${prefix}.vcf.gz.tbi |
nf-test has throws an error with gzipped files that are not actually gzipped
| licence: ["MIT"] | ||
| identifier: "" | ||
| input: | ||
| - - "meta": |
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| - - "meta": | |
| - - meta: |
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.vcf[0][1]).name, |
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Can you test this a little better? You can use the nft-vcf nf-test plugin to easily test VCF files. This plugin is already enabled in this repository so you can immediately start using these methods
| { assert snapshot( | ||
| file(process.out.vcf[0][1]).name, | ||
| process.out.versions).match() } |
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| { assert snapshot( | |
| file(process.out.vcf[0][1]).name, | |
| process.out.versions).match() } | |
| { assert snapshot(process.out).match() } |
Stub tests don't need to be limited as they are empty files
PR checklist
Closes #5976
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockerThis PR implements pypgx/createinputvcf, which creates a vcf file from a bam file, specifically for pharmacogenomics genes