mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
45 lines
1.5 KiB
Text
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), publish_id: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
|
|
"""
|
|
}
|