From b4af3f1475b91d0c411e901d6126515babcdafec Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 15:02:41 +0200
Subject: [PATCH] test fixes

---
 modules/bamtools/split/main.nf       | 9 ++-------
 tests/modules/bamtools/split/main.nf | 9 ++++++---
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f72d13be..7184261e 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,7 +9,6 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
-    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -22,17 +21,13 @@ process BAMTOOLS_SPLIT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
-    if (bam_list) {
-        input_list += " -list $bam_list"
-    }
-    if (!args.contains("-stub")) {
-        args += " -stub ${prefix}"
-    }
+    def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
 
     """
     bamtools merge \\
         ${input_list} \\
     | bamtools split \\
+        $stub \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index ef4b9d59..ff0cb748 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -15,12 +15,15 @@ workflow test_bamtools_split_single_input {
     BAMTOOLS_SPLIT_SINGLE ( input )
 }
 
-workflow test_bamtools_split_multiple_input {
+workflow test_bamtools_split_multiple {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
-    [
+        [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'], checkIfExists: true)]
+
+    ]
 
     BAMTOOLS_SPLIT_MULTIPLE ( input )
 }
+