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a813e2e3a6
* local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
47 lines
1.5 KiB
Text
47 lines
1.5 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_REHEADER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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=1.13" : 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:1.13--h3a49de5_0"
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} else {
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container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
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}
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input:
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tuple val(meta), path(vcf)
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path fai
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path header
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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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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def update_sequences = fai ? "-f $fai" : ""
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def new_header = header ? "-h $header" : ""
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"""
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bcftools \\
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reheader \\
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$update_sequences \\
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$new_header \\
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$options.args \\
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--threads $task.cpus \\
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-o ${prefix}.vcf.gz \\
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$vcf
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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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