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983ba000c1
* Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
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 FGBIO_CALLMOLECULARCONSENSUSREADS {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0"
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} else {
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container "quay.io/biocontainers/fgbio:1.3.0--0"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bam"), emit: bam
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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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fgbio \\
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CallMolecularConsensusReads \\
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-i $bam \\
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$options.args \\
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-o ${prefix}.bam
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fgbio --version | sed -e "s/fgbio v//g" > ${software}.version.txt
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"""
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}
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