nf-core_modules/modules/tiddit/sv/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process TIDDIT_SV {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
} else {
container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
}
input:
tuple val(meta), path(bam)
path fasta
path fai
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output:
tuple val(meta), path("*.vcf") , emit: vcf
tuple val(meta), path("*.ploidy.tab") , emit: ploidy
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tuple val(meta), path("*.signals.tab"), emit: signals
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
"""
tiddit \\
--sv \\
$options.args \\
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--bam $bam \\
$reference \\
-o $prefix
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cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
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"""
}