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Remove commented code
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
This commit is contained in:
Jasmin F
GitHub
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2 changed files with 0 additions and 131 deletions
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@ -1,76 +1,3 @@
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// process ANTISMASH_ANTISMASHLITE {
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// tag "$meta.id"
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// label 'process_medium'
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// conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
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// container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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// 'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
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// 'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
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// containerOptions {
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// workflow.containerEngine == 'singularity' ?
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// "-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
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// workflow.containerEngine == 'docker' ?
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// "-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
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// ''
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// }
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// input:
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// tuple val(meta), path(sequence_input)
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// path(databases)
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// 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).
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// output:
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// tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
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// tuple val(meta), path("${prefix}/css/*.css") , emit: css_file
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// tuple val(meta), path("${prefix}/images") , emit: image_directory
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// tuple val(meta), path("${prefix}/js/*.js") , emit: javascript
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// tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
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// tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
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// tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
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// tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
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// tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
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// tuple val(meta), path("${prefix}/*.json") , emit: json_results
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// tuple val(meta), path("${prefix}/*.log") , emit: log
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// tuple val(meta), path("${prefix}/*.zip") , emit: zip
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// tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
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// tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
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// tuple val(meta), path("${prefix}/index.html") , emit: html
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// tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
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// tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
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// path "versions.yml" , emit: versions
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// when:
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// task.ext.when == null || task.ext.when
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// script:
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// def args = task.ext.args ?: ''
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// prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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// // if ( sequence_input.getExtension != 'fasta' && sequence_input.getExtension != 'fna' && gff )
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// // log.warn "GFF input to antiSMASH can only be used if FASTA sequence input is supplied. GFF will be ignored for sample ${meta.id}"
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// // if ( (sequence_input.getExtension == 'fasta' || sequence_input.getExtension == 'fna') && gff )
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// // gff_flag = "--genefinding-gff3 ${gff}"
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// // else
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// // gff_flag = ""
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// """
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// ## We specifically do not include annotations (--genefinding-tool none) as
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// ## this should be run as a separate module for versioning purposes
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// antismash \\
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// $args \\
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// -c $task.cpus \\
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// --output-dir $prefix \\
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// --genefinding-tool none \\
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// --logfile $prefix/${prefix}.log \\
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// --databases $databases \\
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// $sequence_input
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// cat <<-END_VERSIONS > versions.yml
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// "${task.process}":
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// antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
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// END_VERSIONS
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// """
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// }
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process ANTISMASH_ANTISMASHLITE {
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tag "$meta.id"
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label 'process_medium'
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@ -36,13 +36,6 @@ workflow test_antismashlite {
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
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]
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// input_db = [
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// file('/home/jasmin/antismash_db/', checkIfExists: true)
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// ]
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// input_dir = [
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// file('/home/jasmin/antismash_dir/', checkIfExists: true)
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// ]
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GUNZIP1 ( genome_fna )
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GUNZIP2 ( genome_gff )
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@ -54,54 +47,3 @@ workflow test_antismashlite {
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// ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } )
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}
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// #!/usr/bin/env nextflow
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// nextflow.enable.dsl = 2
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// // include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
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// // include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
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// // include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
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// // // include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
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// include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
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// workflow test_antismashlite {
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// input_genome = [
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// [ id:'test' ], // meta map
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// file('/home/jasmin/Downloads/BAN001-megahit.gbk', checkIfExists: true) ]
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// // input_antismash_db1 = [
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// // [],
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// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
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// // ]
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// // input_antismash_db2 = [
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// // [],
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// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
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// // ]
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// // input_antismash_db3 = [
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// // [],
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// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
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// // ]
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// input_db = [
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// [],
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// file('/home/jasmin/antismash_db/', checkIfExists: true)
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// ]
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// input_dir = [
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// [],
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// file('/home/jasmin/antismash_dir', checkIfExists: true)
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// ]
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// // input_gff = [
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// // [],
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// // file('/home/jasmin/Downloads/BAN001.gff', checkIfExists: true)
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// // ]
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// // UNTAR1 ( input_antismash_db1 )
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// // UNTAR2 ( input_antismash_db2 )
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// // UNTAR3 ( input_antismash_db3 )
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// // ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
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// ANTISMASH_ANTISMASHLITE ( input_genome, input_db, input_dir )
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// }
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