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Fix linting + change test ext args config to match documentation
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prototaxites committed Dec 10, 2024
1 parent f9b6441 commit 9edf6ef
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Showing 3 changed files with 12 additions and 5 deletions.
9 changes: 5 additions & 4 deletions modules/nf-core/dastool/dastool/meta.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,15 @@ input:
type: file
description: fasta file
pattern: "*.{fa.gz,fas.gz,fasta.gz}"
- proteins:
type: file
description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
pattern: "*.{fa.gz,fas.gz,fasta.gz}"

- bins:
type: file
description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin"
pattern: "*.tsv"
- proteins:
type: file
description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
pattern: "*.{fa.gz,fas.gz,fasta.gz}"
- - db_directory:
type: file
description: (optional) Directory of single copy gene database.
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6 changes: 6 additions & 0 deletions modules/nf-core/dastool/dastool/tests/main.nf.test
Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,9 @@ nextflow_process {
test("dastool dastool - bacteroides fragilis - noproteins") {

when {
params {
module_args = '--write_bins --write_bin_evals'
}
process {
"""
input[0] = Channel.of([
Expand Down Expand Up @@ -102,6 +105,9 @@ nextflow_process {
test("dastool dastool - bacteroides fragilis - proteins") {

when {
params {
module_args = '--write_bins --write_bin_evals'
}
process {
"""
input[0] = Channel.of([
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2 changes: 1 addition & 1 deletion modules/nf-core/dastool/dastool/tests/nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: DASTOOL_DASTOOL {
ext.args = "--write_bins --write_bin_evals"
ext.args = params.module_args
}

}

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