mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
35 lines
878 B
Text
35 lines
878 B
Text
process BWA_INDEX {
|
|
tag "$fasta"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' :
|
|
'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }"
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "bwa" , emit: index
|
|
path "versions.yml", emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
mkdir bwa
|
|
bwa \\
|
|
index \\
|
|
$args \\
|
|
-p bwa/${fasta.baseName} \\
|
|
$fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|