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[fix] hicap module allow optional outputs (#937)

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* make hicap outputs optional

* update test data

* typo

* Update main.nf

* use mkfifo

* Update main.nf

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Robert A. Petit III 2021-11-16 02:23:07 -07:00 committed by GitHub
parent d5f6985607
commit bc8899f1bf
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2 changed files with 4 additions and 5 deletions
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7
modules/hicap/main.nf
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@ -24,9 +24,9 @@ process HICAP {
path model_fp
output:
tuple val(meta), path("*.gbk"), emit: gbk
tuple val(meta), path("*.svg"), emit: svg
tuple val(meta), path("*.tsv"), emit: tsv
tuple val(meta), path("*.gbk"), emit: gbk, optional: true
tuple val(meta), path("*.svg"), emit: svg, optional: true
tuple val(meta), path("*.tsv"), emit: tsv, optional: true
path "versions.yml" , emit: versions
script:
@ -39,7 +39,6 @@ process HICAP {
if [ "$is_compressed" == "true" ]; then
gzip -c -d $fasta > $fasta_name
fi
hicap \\
--query_fp $fasta_name \\
$database_args \\

2
tests/modules/hicap/main.nf
View file

@ -7,7 +7,7 @@ include { HICAP } from '../../../modules/hicap/main.nf' addParams( options: [:]
workflow test_hicap {
input = [ [ id:'test', single_end:false ], // meta map
file("https://github.com/bactopia/bactopia-tests/raw/main/data/species-specific/haemophilus-influenzae/GCF_900478275.fna.gz", checkIfExists: true) ]
file("https://github.com/bactopia/bactopia-tests/raw/main/data/species/haemophilus_influenzae/genome/GCF_900478275.fna.gz", checkIfExists: true) ]
database_dir = []
model_fp = []