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44 lines
1.3 KiB
Text
44 lines
1.3 KiB
Text
process IVAR_VARIANTS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
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'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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path gff
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val save_mpileup
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output:
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tuple val(meta), path("*.tsv") , emit: tsv
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tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def features = gff ? "-g $gff" : ""
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def mpileup = save_mpileup ? "tee ${prefix}.mpileup |" : ""
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"""
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samtools mpileup \\
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$args2 \\
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--reference $fasta \\
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$bam | \\
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$mpileup \\
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ivar variants \\
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$args \\
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$features \\
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-r $fasta \\
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-p $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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