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1780cf9bcf
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Add ANGSD doCounts * Prettier * Update main.nf * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Try loosening test due to conda * Remove md5 for binary file Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
process ANGSD_DOCOUNTS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::angsd=0.939" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
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'quay.io/biocontainers/angsd:0.939--h468462d_0' }"
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input:
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tuple val(meta), path(bam), path(bai), path(minqfile)
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output:
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tuple val(meta), path("*.depthSample"), optional: true, emit: depth_sample
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tuple val(meta), path("*.depthGlobal"), optional: true, emit: depth_global
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tuple val(meta), path("*.qs") , optional: true, emit: qs
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tuple val(meta), path("*.pos.gz") , optional: true, emit: pos
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tuple val(meta), path("*.counts.gz") , optional: true, emit: counts
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tuple val(meta), path("*.icnts.gz") , optional: true, emit: icounts
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def minq = minqfile ? "-minQfile ${minqfile}" : ""
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"""
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readlink -f *.bam > bamlist.txt
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angsd \\
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-nThreads ${task.cpus} \\
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-doCounts 1 \\
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$args \\
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-bam bamlist.txt \\
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-out ${prefix} \\
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$minq
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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angsd: \$(echo \$(angsd 2>&1) | grep version | head -n 1 | sed 's/.*version: //g;s/ .*//g')
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END_VERSIONS
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"""
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}
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