nf-core_modules/modules/tiddit/cov/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process TIDDIT_COV {
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::tiddit=2.12.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
} else {
container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
}
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*.tab"), optional: true, emit: cov
tuple val(meta), path("*.wig"), optional: true, emit: wig
path "versions.yml" , emit: versions
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def reference = fasta ? "--ref $fasta" : ""
"""
tiddit \\
--cov \\
-o $prefix \\
$options.args \\
--bam $bam \\
$reference
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
"""
}