nf-core_modules/modules/malt/build/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

58 lines
1.8 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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:[]) }
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0"
} else {
container "quay.io/biocontainers/malt:0.53--hdfd78af_0"
}
input:
path fastas
val seq_type
path gff
path map_db
output:
path "malt_index/" , emit: index
path "versions.yml" , emit: versions
path "malt-build.log", emit: log
script:
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
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2)
END_VERSIONS
"""
}