mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
c5235a983d
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process LAST_LASTAL {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
|
} else {
|
|
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fastx), path (param_file)
|
|
path index
|
|
|
|
output:
|
|
tuple val(meta), path("*.maf.gz"), emit: maf
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def trained_params = param_file ? "-p ${param_file}" : ''
|
|
"""
|
|
INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
|
|
lastal \\
|
|
$trained_params \\
|
|
$options.args \\
|
|
-P $task.cpus \\
|
|
${index}/\$INDEX_NAME \\
|
|
$fastx \\
|
|
| gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
|
|
# gzip needs --no-name otherwise it puts a timestamp in the file,
|
|
# which makes its checksum non-reproducible.
|
|
|
|
echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt
|
|
"""
|
|
}
|