From bc8899f1bf298185a444511d73cdb9dd21ac10f4 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 16 Nov 2021 02:23:07 -0700 Subject: [PATCH] [fix] hicap module allow optional outputs (#937) * make hicap outputs optional * update test data * typo * Update main.nf * use mkfifo * Update main.nf Co-authored-by: Gisela Gabernet Co-authored-by: FriederikeHanssen Co-authored-by: Harshil Patel --- modules/hicap/main.nf | 7 +++---- tests/modules/hicap/main.nf | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/modules/hicap/main.nf b/modules/hicap/main.nf index e2e70678..fbc157b1 100644 --- a/modules/hicap/main.nf +++ b/modules/hicap/main.nf @@ -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 \\ diff --git a/tests/modules/hicap/main.nf b/tests/modules/hicap/main.nf index 77c309a5..3ac9c20b 100644 --- a/tests/modules/hicap/main.nf +++ b/tests/modules/hicap/main.nf @@ -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 = []