nf-core_modules/modules/maltextract/main.nf
James A. Fellows Yates 7830a4a80c
add: MALTEXTRACT (#725)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start maltextract module

* start tests

* Get tests working now we have test data

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Changes after review

* Update tests/modules/maltextract/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/maltextract/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/maltextract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-21 19:57:27 +01:00

44 lines
1.3 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MALTEXTRACT {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
} else {
container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
}
input:
path rma6
path taxon_list
path ncbi_dir
output:
path "results" , emit: results
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
MaltExtract \\
-Xmx${task.memory.toGiga()}g \\
-p $task.cpus \\
-i ${rma6.join(' ')} \\
-t $taxon_list \\
-r $ncbi_dir \\
-o results/ \\
$options.args
echo \$(MaltExtract --help | head -n 2 | tail -n 1) | sed 's/MaltExtract version//' > ${software}.version.txt
"""
}