nf-core_modules/software/tiddit/sv/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

45 lines
1.5 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process TIDDIT_SV {
tag "$meta.id"
label 'process_medium'
publishDir "${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
path fai
output:
tuple val(meta), path("*.vcf"), emit: vcf
tuple val(meta), path("*.ploidy.tab"), emit: ploidy
tuple val(meta), path("*.signals.tab"), emit: signals
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def output = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
"""
tiddit \\
--sv $options.args \\
--bam $bam \\
$reference \\
-o $output
echo \$(tiddit -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
"""
}