nf-core_modules/modules/malt/build/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MALT_BUILD {
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
// Do not **auto-bump** due to problem with change of version numbering between 0.4.1 and 0.5.2
// (originally 0.4.1 was listed as 0.41, so is always selected as 'latest' even though it is not!)
conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0"
} else {
container "quay.io/biocontainers/malt:0.5.2--0"
}
input:
path fastas
val seq_type
path gff
path map_db
output:
path "malt_index/" , emit: index
path "*.version.txt" , emit: version
path "malt-build.log", emit: log
script:
def software = getSoftwareName(task.process)
def avail_mem = 6
if (!task.memory) {
log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
def igff = gff ? "-igff ${gff}" : ""
"""
malt-build \\
-J-Xmx${avail_mem}g \\
-v \\
--input ${fastas.join(' ')} \\
-s $seq_type \\
$igff \\
-d 'malt_index/' \\
-t ${task.cpus} \\
$options.args \\
-mdb ${map_db}/*.db |&tee malt-build.log
malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2 > ${software}.version.txt
"""
}