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Streamlined some output channels, formatted tests main.nf
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3 changed files with 4 additions and 17 deletions
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@ -23,9 +23,7 @@ process ANTISMASH_ANTISMASHLITE {
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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("${prefix}/{css,images,js}") , emit: html_accessory_files
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tuple val(meta), path("${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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@ -67,18 +67,10 @@ output:
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type: file
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description: Output of ClusterBlast algorithm
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pattern: "clusterblast/*_c*.txt"
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- css_file:
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type: file
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description: Style sheet containing the formatting of HTML output
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pattern: "css/*.css"
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- image_directory:
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- html_accessory_files:
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type: directory
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description: image files for web view of antiSMASH results
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pattern: "images"
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- javascript:
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type: file
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description: JavaScript files
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pattern: "js/*.js"
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description: Accessory files for the HTML output
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pattern: "{css/,images/,js/}"
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- knownclusterblast_html:
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type: file
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description: Tables with MIBiG hits in HTML format
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@ -36,7 +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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GUNZIP1 ( genome_fna )
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GUNZIP2 ( genome_gff )
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UNTAR1 ( antismash_db1 )
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@ -44,6 +43,4 @@ workflow test_antismashlite {
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UNTAR3 ( 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 ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
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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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