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55 lines
1.6 KiB
Text
55 lines
1.6 KiB
Text
process TIDDIT_SV {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::tiddit=3.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tiddit:3.1.0--py39h59fae87_1' :
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'quay.io/biocontainers/tiddit:3.1.0--py39h59fae87_1' }"
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input:
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tuple val(meta), path(input), path(input_index)
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path fasta
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path bwa_index
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output:
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tuple val(meta), path("*.vcf") , emit: vcf
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tuple val(meta), path("*.ploidies.tab"), emit: ploidy
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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 bwa_command = bwa_index ? "[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! \"\$i\" =~ .*\"$fasta\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : ""
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"""
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$bwa_command
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tiddit \\
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--sv \\
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$args \\
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--bam $input \\
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--ref $fasta \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.vcf
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touch ${prefix}.ploidies.tab
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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