nf-core_modules/modules/macrel/contigs/main.nf

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process MACREL_CONTIGS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0':
'quay.io/biocontainers/macrel:1.1.0--py36hc5360cc_0' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("*/*.smorfs.faa.gz") , emit: smorfs
tuple val(meta), path("*/*.all_orfs.faa.gz") , emit: all_orfs
tuple val(meta), path("*/*.prediction.gz") , emit: amp_prediction
tuple val(meta), path("*/*.md") , emit: readme_file
tuple val(meta), path("*/*_log.txt") , emit: log_file
path "versions.yml" , emit: versions
2022-02-04 08:53:32 +00:00
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
macrel contigs \\
$args \\
--fasta $fasta \\
--output ${prefix}/ \\
--tag ${prefix} \\
--log-file ${prefix}/${prefix}_log.txt \\
--threads $task.cpus
gzip --no-name ${prefix}/*.faa
cat <<-END_VERSIONS > versions.yml
"${task.process}":
macrel: \$(echo \$(macrel --version | sed 's/macrel //g'))
END_VERSIONS
"""
}