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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BCFTOOLS_MPILEUP {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
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} else {
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container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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tuple val(meta), path("*stats.txt"), emit: stats
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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echo "${meta.id}" > sample_name.list
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bcftools mpileup \\
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--fasta-ref $fasta \\
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$options.args \\
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$bam \\
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| bcftools call --output-type v $options.args2 \\
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| bcftools reheader --samples sample_name.list \\
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| bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
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tabix -p vcf -f ${prefix}.vcf.gz
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bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
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echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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