mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
4619d012e5
* Add CRAM support to allelecounter * Update meta.yml * Rename bam,bai to input,input_index * Apply suggestions from code review * Fix reference to renamed variable Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
47 lines
1.5 KiB
Text
47 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ALLELECOUNTER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
|
|
} else {
|
|
container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(input), path(input_index)
|
|
path loci
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("*.alleleCount"), emit: allelecount
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def reference_options = fasta ? "-r $fasta": ""
|
|
|
|
"""
|
|
alleleCounter \\
|
|
$options.args \\
|
|
-l $loci \\
|
|
-b $input \\
|
|
$reference_options \\
|
|
-o ${prefix}.alleleCount
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(alleleCounter --version)
|
|
END_VERSIONS
|
|
"""
|
|
}
|