nf-core_modules/modules/lofreq/callparallel/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process LOFREQ_CALLPARALLEL {
tag "$meta.id"
label 'process_high'
publishDir "${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::lofreq=2.1.5" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
} else {
container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
lofreq \\
call-parallel \\
--pp-threads $task.cpus \\
$options.args \\
-f $fasta \\
-o ${prefix}.vcf.gz \\
$bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}