From 45b4a61a15c8b7ac6c29a447ccc1ece9f08f8efe Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 13:31:37 +0200
Subject: [PATCH] Some small updates

---
 modules/vardictjava/main.nf        | 2 +-
 tests/modules/vardictjava/main.nf  | 8 ++++----
 tests/modules/vardictjava/test.yml | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index c370b6ef..26833436 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -30,7 +30,7 @@ process VARDICTJAVA {
         -th $task.cpus \\
         -N $prefix \\
         -G $reference_fasta \\
-        $regions_of_interest
+        $regions_of_interest \\
         | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index 89eec407..d392358a 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -6,15 +6,15 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
 
 workflow test_vardictjava {
     
-    bam_input_ch = Channel.of([
-        [ id:'test', single_end:false ], // meta map
+    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)
     ])
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
 
-    reference = Channel.of([
+    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)
     ])
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 77aa9047..0bd21f4e 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 2179dcaee6183495b421293f42db11b5
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96