nf-core_modules/modules/allelecounter/main.nf
fbdtemme 4619d012e5
Add cram support to Allelecounter module (#1013)
* 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>
2021-11-02 17:00:25 +01:00

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// 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
"""
}