mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
75 lines
4 KiB
Text
75 lines
4 KiB
Text
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' }"
|
|
|
|
containerOptions {
|
|
workflow.containerEngine == 'singularity' ?
|
|
"-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
|
|
workflow.containerEngine == 'docker' ?
|
|
"-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
|
|
''
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(sequence_input)
|
|
path(gff)
|
|
path(databases)
|
|
path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
|
|
|
|
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}"
|
|
if ( sequence_input.getExtension != 'fasta' && sequence_input.getExtension != 'fna' && gff )
|
|
log.warn "GFF input to antiSMASH can only be used if FASTA sequence input is supplied. GFF will be ignored for sample ${meta.id}"
|
|
if ( (sequence_input.getExtension == 'fasta' || sequence_input.getExtension == 'fna') && gff )
|
|
gff_flag = "--genefinding-gff3 ${gff}"
|
|
else
|
|
gff_flag = ""
|
|
|
|
"""
|
|
## We specifically do not include annotations (--genefinding-tool none) as
|
|
## this should be run as a separate module for versioning purposes
|
|
antismash \\
|
|
$args \\
|
|
-c $task.cpus \\
|
|
--output-dir $prefix \\
|
|
--genefinding-tool none \\
|
|
--logfile $prefix/${prefix}.log \\
|
|
--databases $databases \\
|
|
$gff_flag \\
|
|
$sequence_input
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|