nf-core_modules/modules/picard/collectmultiplemetrics/main.nf
2022-05-21 08:33:49 +02:00

66 lines
2.4 KiB
Text

process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*_metrics"), emit: metrics
tuple val(meta), path("*.pdf") , emit: pdf
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 reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
CollectMultipleMetrics \\
$args \\
--INPUT $bam \\
--OUTPUT ${prefix}.CollectMultipleMetrics \\
$reference
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}