nf-core_modules/modules/bowtie/build/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

37 lines
1.2 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process BOWTIE_BUILD {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
} else {
container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
}
input:
path fasta
output:
path 'bowtie' , emit: index
path "versions.yml" , emit: versions
script:
"""
mkdir bowtie
bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
END_VERSIONS
"""
}