mirror of
https://github.com/MillironX/nf-core_modules.git
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37 lines
1,015 B
Text
37 lines
1,015 B
Text
process LOFREQ_CALL {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
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'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
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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("*.vcf.gz"), emit: vcf
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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 ?: "${meta.id}"
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"""
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lofreq \\
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call \\
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$args \\
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-f $fasta \\
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-o ${prefix}.vcf.gz \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
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END_VERSIONS
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"""
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}
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