mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
43 lines
1.5 KiB
Text
43 lines
1.5 KiB
Text
|
// 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
|
||
|
|
"""
|
||
|
|
}
|