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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Jasmin F 2022-05-12 15:28:19 +02:00 committed by GitHub
parent 3c02e6056c
commit 85b3c2bcf2
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2 changed files with 13 additions and 13 deletions
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12
modules/antismash/antismashlite/meta.yml
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@ -48,10 +48,10 @@ input:
be done in immutable docker/singularity containers. Therefore, a local installation
directory needs to be mounted (including all modified files from the downloading step)
to the container as a workaround.
pattern: "*"
pattern: "*/"
- gff:
type: file
pattern: "*.gff"
type: file
pattern: "*.gff"
output:
- meta:
@ -89,11 +89,11 @@ output:
pattern: "svg/knownclusterblast*.svg"
- gbk_input:
type: file
description: Nucleotide sequence + annotations in GenBank format; converted from input file
description: Nucleotide sequence and annotations in GenBank format; converted from input file
pattern: "*.gbk"
- json_results:
type: file
description: Nucleotide sequence + annotations in JSON format; converted from GenBank file (gbk_input)
description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
pattern: "*.json"
- log:
type: file
@ -105,7 +105,7 @@ output:
pattern: "*.zip"
- gbk_results:
type: file
description: Nucleotide sequence + annotations in GenBank format; one file per antiSMASH hit
description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit
pattern: "*region*.gbk"
- clusterblastoutput:
type: file

14
tests/modules/antismash/antismashlite/main.nf
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf'
@ -21,26 +21,26 @@ workflow test_antismashlite {
file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
]
antismash_db1 = [
antismash_css = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
antismash_db2 = [
antismash_detection = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
antismash_db3 = [
antismash_modules = [
[],
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 )
UNTAR2 ( antismash_db2 )
UNTAR3 ( antismash_db3 )
UNTAR1 ( antismash_css )
UNTAR2 ( antismash_detection )
UNTAR3 ( antismash_modules )
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] } )
}