diff --git a/modules/antismash/antismashlite/main.nf b/modules/antismash/antismashlite/main.nf index fb8def97..6f43c6d7 100644 --- a/modules/antismash/antismashlite/main.nf +++ b/modules/antismash/antismashlite/main.nf @@ -1,76 +1,3 @@ -// 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(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 \\ -// $sequence_input - -// cat <<-END_VERSIONS > versions.yml -// "${task.process}": -// antismash-lite: \$(antismash --version | sed 's/antiSMASH //') -// END_VERSIONS -// """ -// } process ANTISMASH_ANTISMASHLITE { tag "$meta.id" label 'process_medium' diff --git a/tests/modules/antismash/antismashlite/main.nf b/tests/modules/antismash/antismashlite/main.nf index 02f9e0f9..50627590 100644 --- a/tests/modules/antismash/antismashlite/main.nf +++ b/tests/modules/antismash/antismashlite/main.nf @@ -36,13 +36,6 @@ workflow test_antismashlite { file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) ] - // input_db = [ - // file('/home/jasmin/antismash_db/', checkIfExists: true) - // ] - - // input_dir = [ - // file('/home/jasmin/antismash_dir/', checkIfExists: true) - // ] GUNZIP1 ( genome_fna ) GUNZIP2 ( genome_gff ) @@ -54,54 +47,3 @@ workflow test_antismashlite { // ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } ) } -// #!/usr/bin/env nextflow - -// nextflow.enable.dsl = 2 - -// // include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf' -// // include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf' -// // include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf' -// // // include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf' -// include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf' - -// workflow test_antismashlite { -// input_genome = [ -// [ id:'test' ], // meta map -// file('/home/jasmin/Downloads/BAN001-megahit.gbk', checkIfExists: true) ] - -// // input_antismash_db1 = [ -// // [], -// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true) -// // ] - -// // input_antismash_db2 = [ -// // [], -// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true) -// // ] - -// // input_antismash_db3 = [ -// // [], -// // file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) -// // ] - -// input_db = [ -// [], -// file('/home/jasmin/antismash_db/', checkIfExists: true) -// ] - -// input_dir = [ -// [], -// file('/home/jasmin/antismash_dir', checkIfExists: true) -// ] - -// // input_gff = [ -// // [], -// // file('/home/jasmin/Downloads/BAN001.gff', checkIfExists: true) -// // ] - -// // UNTAR1 ( input_antismash_db1 ) -// // UNTAR2 ( input_antismash_db2 ) -// // UNTAR3 ( input_antismash_db3 ) -// // ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } ) -// ANTISMASH_ANTISMASHLITE ( input_genome, input_db, input_dir ) -// }