From b35264e9196d8f7c74c28a7bd5bc126a5e16afe8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:11:37 +0200
Subject: [PATCH] bugfixes

---
 modules/bamtools/split/main.nf       | 6 ++----
 modules/bamtools/split/meta.yml      | 2 +-
 tests/modules/bamtools/split/main.nf | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f6382d97..2f5ef09f 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -20,7 +20,6 @@ process BAMTOOLS_SPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
     if (bam_list) {
@@ -30,9 +29,8 @@ process BAMTOOLS_SPLIT {
     """
     bamtools merge \\
         ${input_list} \\
-        $args \\
-    bamtools split \\
-        $args2
+    | bamtools split \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 6c534281..0fd5d5ca 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -28,7 +28,7 @@ input:
   - bam_list:
       type: file
       description: |
-        Input file containing bam files to merge before splitting,
+        Optional input file containing bam files to merge before splitting,
         one line per file
 
 output:
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index eb0bed01..9f30c4f9 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -10,5 +10,5 @@ workflow test_bamtools_split {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT ( input, [] )
 }