From 96d4a31cc15e3b20ee6a7df0ad39ca59feeb3a02 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 3 May 2022 15:31:05 +0200 Subject: [PATCH] Moved the BED file to the main tuple --- modules/vardictjava/main.nf | 3 +-- tests/modules/vardictjava/main.nf | 7 +++---- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf index 454b86a4..c99301bb 100644 --- a/modules/vardictjava/main.nf +++ b/modules/vardictjava/main.nf @@ -10,8 +10,7 @@ process VARDICTJAVA { 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" input: - tuple val(meta), path(bam), path(bai) - path(bed) + tuple val(meta), path(bam), path(bai), path(bed) tuple path(fasta), path(fasta_fai) output: diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf index d392358a..e29490f3 100644 --- a/tests/modules/vardictjava/main.nf +++ b/tests/modules/vardictjava/main.nf @@ -9,15 +9,14 @@ workflow test_vardictjava { bam_input_ch = Channel.value([ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]) - bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)) - reference = Channel.value([ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ]) - VARDICTJAVA ( bam_input_ch, bed, reference ) + VARDICTJAVA ( bam_input_ch, reference ) }