nf-core_modules/software/bwamem2/index/main.nf
Jose Espinosa-Carrasco 572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00

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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BWAMEM2_INDEX {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.1--he513fc3_0"
} else {
container "quay.io/biocontainers/bwa-mem2:2.1--he513fc3_0"
}
input:
path fasta
output:
path "bwamem2" , emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
mkdir bwamem2
bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
"""
}