mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
34 lines
856 B
Text
34 lines
856 B
Text
process CHROMAP_INDEX {
|
|
tag '$fasta'
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
|
|
'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }"
|
|
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "*.index" , emit: index
|
|
path "versions.yml", emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = fasta.baseName
|
|
"""
|
|
chromap \\
|
|
-i \\
|
|
$args \\
|
|
-t $task.cpus \\
|
|
-r $fasta \\
|
|
-o ${prefix}.index
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
chromap: \$(echo \$(chromap --version 2>&1))
|
|
END_VERSIONS
|
|
"""
|
|
}
|