nf-core_modules/software/bwa/mem/main.nf
2020-08-05 17:16:08 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process BWA_MEM {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
//container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
conda (params.conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.10" : null)
input:
tuple val(meta), path(reads)
path index
path fasta
val options
output:
tuple val(meta), path("*.bam"), emit: bam
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
def rg = meta.read_group ? "-R ${meta.read_group}" : ""
"""
bwa mem \\
$ioptions.args \\
$rg \\
-t $task.cpus \\
$fasta \\
$reads \\
| samtools view $ioptions.args2 -@ $task.cpus -bS -o ${prefix}.bam -
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
}