nf-core_modules/modules/freebayes/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FREEBAYES {
tag "$meta.id"
label 'process_low'
publishDir "${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::freebayes=1.3.5" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3"
} else {
container "quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3"
}
input:
tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index)
path fasta
path fai
path targets
path samples
path populations
path cnv
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input = input_2 ? "${input_1} ${input_2}" : "${input_1}"
def targets_file = targets ? "--target ${targets}" : ""
def samples_file = samples ? "--samples ${samples}" : ""
def populations_file = populations ? "--populations ${populations}" : ""
def cnv_file = cnv ? "--cnv-map ${cnv}" : ""
if (task.cpus > 1) {
"""
freebayes-parallel \\
<(fasta_generate_regions.py ${fasta}.fai 10000) ${task.cpus} \\
-f $fasta \\
$targets_file \\
$samples_file \\
$populations_file \\
$cnv_file \\
$options.args \\
$input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
END_VERSIONS
"""
} else {
"""
freebayes \\
-f $fasta \\
$targets_file \\
$samples_file \\
$populations_file \\
$cnv_file \\
$options.args \\
$input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
END_VERSIONS
"""
}
}