mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 19:48:16 +00:00
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process LAST_LASTAL {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
|
|
'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 "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 trained_params = param_file ? "-p ${param_file}" : ''
|
|
"""
|
|
INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
|
|
lastal \\
|
|
$trained_params \\
|
|
$args \\
|
|
-P $task.cpus \\
|
|
${index}/\$INDEX_NAME \\
|
|
$fastx \\
|
|
| gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
|
|
# gzip needs --no-name otherwise it puts a timestamp in the file,
|
|
# which makes its checksum non-reproducible.
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
last: \$(lastal --version 2>&1 | sed 's/lastal //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|