mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
47 lines
1.5 KiB
Text
47 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process GATK4_CREATESEQUENCEDICTIONARY {
|
|
tag "$fasta"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
|
|
} else {
|
|
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
|
|
}
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "*.dict" , emit: dict
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def avail_mem = 6
|
|
if (!task.memory) {
|
|
log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" \\
|
|
CreateSequenceDictionary \\
|
|
--REFERENCE $fasta \\
|
|
--URI $fasta \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|