nf-core_modules/modules/antismash/antismashlite/main.nf

59 lines
3.1 KiB
Text
Raw Normal View History

2022-04-22 14:47:48 +00:00
process ANTISMASH_ANTISMASHLITE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
input:
tuple val(meta), path(sequence_input)
path(databases)
output:
tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
tuple val(meta), path("$prefix/css/*.css") , emit: css_file
tuple val(meta), path("$prefix/images") , emit: image_directory
tuple val(meta), path("$prefix/js/*.js") , emit: javascript
tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
tuple val(meta), path("$prefix/*.gbk") , emit: gbk_input
tuple val(meta), path("$prefix/*.json") , emit: json_results
tuple val(meta), path("$prefix/*.log") , emit: log
tuple val(meta), path("$prefix/*.zip") , emit: zip
tuple val(meta), path("$prefix/*region*.gbk") , emit: gbk_results
tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
tuple val(meta), path("$prefix/index.html") , emit: html
tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
tuple val(meta), path("$prefix/regions.js") , emit: json_sideloading
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
## We specifically do not include annotations (--genefinding-tool none) as
## this should be run as a separate module for versioning purposes
antismash \\
$sequence_input \\
$args \\
-c $task.cpus \\
--output-dir $prefix \\
--genefinding-tool none \\
--logfile $prefix/${prefix}.log \\
--databases $databases
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash: \$(antismash --version | sed 's/antiSMASH //')
END_VERSIONS
"""
}