nf-core_modules/modules/sequenzautils/bam2seqz/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SEQUENZAUTILS_BAM2SEQZ {
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']) }
conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2"
} else {
container "quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2"
}
input:
tuple val(meta), path(normalbam), path(tumourbam)
path fasta
path wigfile
output:
tuple val(meta), path("*.seqz.gz"), emit: seqz
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
sequenza-utils \\
bam2seqz \\
$options.args \\
-n $normalbam \\
-t $tumourbam \\
--fasta $fasta \\
-gc $wigfile \\
-o ${prefix}.seqz.gz
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//')
END_VERSIONS
"""
}