mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
57 lines
2.1 KiB
Text
57 lines
2.1 KiB
Text
|
process GATK4_COLLECTSVEVIDENCE {
|
||
|
|
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(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi)
|
||
|
|
path fasta
|
||
|
|
path fasta_fai
|
||
|
|
path dict
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.sr.txt.gz") , emit: split_read_evidence
|
||
|
|
tuple val(meta), path("*.sr.txt.gz.tbi"), emit: split_read_evidence_index
|
||
|
|
tuple val(meta), path("*.pe.txt.gz") , emit: paired_end_evidence
|
||
|
|
tuple val(meta), path("*.pe.txt.gz.tbi"), emit: paired_end_evidence_index
|
||
|
|
tuple val(meta), path("*.ld.txt.gz") , emit: allele_counts, optional:true
|
||
|
|
tuple val(meta), path("*.ld.txt.gz.tbi"), emit: allele_counts_index, optional:true
|
||
|
|
path "versions.yml" , emit: versions
|
||
|
|
|
||
|
|
when:
|
||
|
|
task.ext.when == null || task.ext.when
|
||
|
|
|
||
|
|
script:
|
||
|
|
def args = task.ext.args ?: ''
|
||
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||
|
|
|
||
|
|
def allele_vcf = allele_count_vcf ? "--allele-count-file ${prefix}.ld.txt.gz --allele-count-vcf ${allele_count_vcf}" : ""
|
||
|
|
def reference = fasta ? "--reference ${fasta}" : ""
|
||
|
|
|
||
|
|
def avail_mem = 3
|
||
|
|
if (!task.memory) {
|
||
|
|
log.info '[GATK COLLECTSVEVIDENCE] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||
|
|
} else {
|
||
|
|
avail_mem = task.memory.giga
|
||
|
|
}
|
||
|
|
"""
|
||
|
|
gatk --java-options "-Xmx${avail_mem}g" CollectSVEvidence \\
|
||
|
|
${args} \\
|
||
|
|
--input ${input} \\
|
||
|
|
--sr-file ${prefix}.sr.txt.gz \\
|
||
|
|
--pe-file ${prefix}.pe.txt.gz \\
|
||
|
|
${allele_vcf} \\
|
||
|
|
${reference} \\
|
||
|
|
--tmp-dir . \\
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|