nf-core_modules/software/bwa/index/main.nf

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2020-08-05 16:15:56 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process BWA_INDEX {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
container "biocontainers/bwa:v0.7.17_cv1"
//container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
conda (params.conda ? "bioconda::bwa=0.7.17" : null)
input:
path fasta
val options
output:
path "${fasta}.*", emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
"""
bwa index $ioptions.args $fasta
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
"""
}