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f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
73 lines
2.3 KiB
Text
73 lines
2.3 KiB
Text
process FREEBAYES {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3' :
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'quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3' }"
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input:
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tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed)
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path fasta
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path fasta_fai
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path samples
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path populations
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path cnv
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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 ?: "${meta.id}"
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def input = input_2 ? "${input_1} ${input_2}" : "${input_1}"
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def targets_file = target_bed ? "--target ${target_bed}" : ""
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def samples_file = samples ? "--samples ${samples}" : ""
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def populations_file = populations ? "--populations ${populations}" : ""
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def cnv_file = cnv ? "--cnv-map ${cnv}" : ""
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if (task.cpus > 1) {
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"""
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freebayes-parallel \\
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<(fasta_generate_regions.py $fasta_fai 10000) $task.cpus \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$populations_file \\
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$cnv_file \\
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$args \\
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$input > ${prefix}.vcf
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bgzip ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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freebayes: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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} else {
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"""
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freebayes \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$populations_file \\
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$cnv_file \\
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$args \\
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$input > ${prefix}.vcf
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bgzip ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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freebayes: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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}
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}
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