mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +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
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BEDTOOLS_GETFASTA {
|
|
tag "$bed"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
|
|
|
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
|
} else {
|
|
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
|
|
}
|
|
|
|
input:
|
|
path bed
|
|
path fasta
|
|
|
|
output:
|
|
path "*.fa" , emit: fasta
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
|
|
"""
|
|
bedtools \\
|
|
getfasta \\
|
|
$options.args \\
|
|
-fi $fasta \\
|
|
-bed $bed \\
|
|
-fo ${prefix}.fa
|
|
|
|
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
|
|
"""
|
|
}
|