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Streamlined some output channels, formatted tests main.nf

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jasmezz 2022-05-12 10:56:48 +02:00
parent 853e3ec087
commit bd4b70439b
3 changed files with 4 additions and 17 deletions
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4
modules/antismash/antismashlite/main.nf
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@ -23,9 +23,7 @@ process ANTISMASH_ANTISMASHLITE {
output: output:
tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
tuple val(meta), path("${prefix}/css/*.css") , emit: css_file tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files
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/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}/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/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast

14
modules/antismash/antismashlite/meta.yml
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@ -67,18 +67,10 @@ output:
type: file type: file
description: Output of ClusterBlast algorithm description: Output of ClusterBlast algorithm
pattern: "clusterblast/*_c*.txt" pattern: "clusterblast/*_c*.txt"
- css_file: - html_accessory_files:
type: file
description: Style sheet containing the formatting of HTML output
pattern: "css/*.css"
- image_directory:
type: directory type: directory
description: image files for web view of antiSMASH results description: Accessory files for the HTML output
pattern: "images" pattern: "{css/,images/,js/}"
- javascript:
type: file
description: JavaScript files
pattern: "js/*.js"
- knownclusterblast_html: - knownclusterblast_html:
type: file type: file
description: Tables with MIBiG hits in HTML format description: Tables with MIBiG hits in HTML format

3
tests/modules/antismash/antismashlite/main.nf
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@ -36,7 +36,6 @@ workflow test_antismashlite {
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
] ]
GUNZIP1 ( genome_fna ) GUNZIP1 ( genome_fna )
GUNZIP2 ( genome_gff ) GUNZIP2 ( genome_gff )
UNTAR1 ( antismash_db1 ) UNTAR1 ( antismash_db1 )
@ -44,6 +43,4 @@ workflow test_antismashlite {
UNTAR3 ( antismash_db3 ) UNTAR3 ( antismash_db3 )
ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } ) ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } ) ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
// ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } )
} }