Streamlined some output channels, formatted tests main.nf

This commit is contained in:
jasmezz 2022-05-12 10:56:48 +02:00
parent 853e3ec087
commit bd4b70439b
3 changed files with 4 additions and 17 deletions

View file

@ -23,9 +23,7 @@ process ANTISMASH_ANTISMASHLITE {
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("${prefix}/{css,images,js}") , emit: html_accessory_files
tuple val(meta), path("${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

View file

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

View file

@ -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)
]
GUNZIP1 ( genome_fna )
GUNZIP2 ( genome_gff )
UNTAR1 ( antismash_db1 )
@ -44,6 +43,4 @@ workflow test_antismashlite {
UNTAR3 ( antismash_db3 )
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, input_db, input_dir, GUNZIP2.out.gunzip.map{ it[1] } )
}