nf-core_modules/modules/malt/run/main.nf
James A. Fellows Yates 72b96f4e50
Add missing $prefix definition for MALT_RUN (#1373)
* fix: remove left-over unnecessary code

* Add forgotten prefix for the log

* Update meta.yml

* Update tests

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-03 17:58:04 +01:00

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1.5 KiB
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process MALT_RUN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
input:
tuple val(meta), path(fastqs)
val mode
path index
output:
tuple val(meta), path("*.rma6") , emit: rma6
tuple val(meta), path("*.{tab,text,sam}"), optional:true, emit: alignments
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 6
if (!task.memory) {
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
malt-run \\
-J-Xmx${avail_mem}g \\
-t $task.cpus \\
-v \\
-o . \\
$args \\
--inFile ${fastqs.join(' ')} \\
-m $mode \\
--index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
malt: \$(malt-run --help 2>&1 | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ')
END_VERSIONS
"""
}