From 07982d6cb13649c308625bb3d215c39979e1207c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:31:39 +0200
Subject: [PATCH] fix command line, fix meta.yml

---
 modules/bamtools/split/main.nf        | 5 ++++-
 tests/modules/bamtools/split/test.yml | 9 +++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 2f5ef09f..f72d13be 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -23,7 +23,10 @@ process BAMTOOLS_SPLIT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
     if (bam_list) {
-        input += " -list $bam_list"
+        input_list += " -list $bam_list"
+    }
+    if (!args.contains("-stub")) {
+        args += " -stub ${prefix}"
     }
 
     """
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 4f52e9ce..b52cc9ee 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,10 +1,11 @@
 - name: bamtools split test_bamtools_split
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
   tags:
-    - bamtools/split
     - bamtools
+    - bamtools/split
   files:
-    - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
+    - path: output/bamtools/test.REF_chr22.bam
       md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
+    - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml