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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 be done in immutable docker/singularity containers. Therefore, a local installation
directory needs to be mounted (including all modified files from the downloading step) directory needs to be mounted (including all modified files from the downloading step)
to the container as a workaround. to the container as a workaround.
pattern: "*" pattern: "*/"
- gff: - gff:
type: file type: file
pattern: "*.gff" pattern: "*.gff"
output: output:
- meta: - meta:
@ -89,11 +89,11 @@ output:
pattern: "svg/knownclusterblast*.svg" pattern: "svg/knownclusterblast*.svg"
- gbk_input: - gbk_input:
type: file 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" pattern: "*.gbk"
- json_results: - json_results:
type: file 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" pattern: "*.json"
- log: - log:
type: file type: file
@ -105,7 +105,7 @@ output:
pattern: "*.zip" pattern: "*.zip"
- gbk_results: - gbk_results:
type: file 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" pattern: "*region*.gbk"
- clusterblastoutput: - clusterblastoutput:
type: file type: file

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

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 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 { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf' include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
include { GUNZIP as GUNZIP2 } 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) 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) 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) 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) 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_css )
UNTAR2 ( antismash_db2 ) UNTAR2 ( antismash_detection )
UNTAR3 ( antismash_db3 ) UNTAR3 ( antismash_modules )
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] } )
} }