mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
67 lines
2.5 KiB
Text
67 lines
2.5 KiB
Text
process GATK4_GENOMICSDBIMPORT {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
|
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
|
|
val run_intlist
|
|
val run_updatewspace
|
|
val input_map
|
|
|
|
output:
|
|
tuple val(meta), path("$prefix") , optional:true, emit: genomicsdb
|
|
tuple val(meta), path("$updated_db") , optional:true, emit: updatedb
|
|
tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
|
|
// settings for running default create gendb mode
|
|
input_command = input_map ? "--sample-name-map ${vcf[0]}" : vcf.collect(){"--variant $it"}.join(' ')
|
|
|
|
genomicsdb_command = "--genomicsdb-workspace-path ${prefix}"
|
|
interval_command = interval_file ? "--intervals ${interval_file}" : "--intervals ${interval_value}"
|
|
|
|
// settings changed for running get intervals list mode if run_intlist is true
|
|
if (run_intlist) {
|
|
genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}"
|
|
interval_command = "--output-interval-list-to-file ${prefix}.interval_list"
|
|
}
|
|
|
|
// settings changed for running update gendb mode. input_command same as default, update_db forces module to emit the updated gendb
|
|
if (run_updatewspace) {
|
|
genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}"
|
|
interval_command = ''
|
|
updated_db = "${wspace}"
|
|
}
|
|
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK GenomicsDBImport] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" GenomicsDBImport \\
|
|
$input_command \\
|
|
$genomicsdb_command \\
|
|
$interval_command \\
|
|
--tmp-dir . \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|