mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
e726b1730d
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
57 lines
1.8 KiB
Text
57 lines
1.8 KiB
Text
process GATK4_MARKDUPLICATES {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
|
container "${ 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(bam)
|
|
path fasta
|
|
path fasta_fai
|
|
|
|
output:
|
|
tuple val(meta), path("*cram"), emit: cram, optional: true
|
|
tuple val(meta), path("*bam"), emit: bam, optional: true
|
|
tuple val(meta), path("*.crai"), emit: crai, optional: true
|
|
tuple val(meta), path("*.bai"), emit: bai, optional: true
|
|
tuple val(meta), path("*.metrics"), emit: metrics
|
|
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}"
|
|
def input_list = bam.collect{"--INPUT $it"}.join(' ')
|
|
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
|
|
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\
|
|
$input_list \\
|
|
--OUTPUT ${prefix} \\
|
|
--METRICS_FILE ${prefix}.metrics \\
|
|
--TMP_DIR . \\
|
|
${reference} \\
|
|
$args
|
|
|
|
|
|
if [[ ${prefix} == *.cram ]]; then
|
|
mv ${prefix}.bai ${prefix}.crai
|
|
fi
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|