From fefffb9bb0776e679c2297e8d80325d57e2f2d7a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 12:36:32 +0200
Subject: [PATCH] fix output glob

---
 modules/elprep/merge/main.nf        | 6 +++---
 tests/modules/elprep/merge/test.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 2b12bfe2..28fa9985 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -11,8 +11,8 @@ process ELPREP_MERGE {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}")   , emit: bam
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("output/**.{bam,sam}")    , emit: bam
+    path "versions.yml"                             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,7 +30,7 @@ process ELPREP_MERGE {
 
     elprep merge \\
         input \\
-        ${prefix}.${suffix} \\
+        output/${prefix}.${suffix} \\
         $args \\
         ${single_end} \\
         --nr-of-threads $task.cpus
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index d6037bec..ad2ecfef 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -4,5 +4,5 @@
     - elprep
     - elprep/merge
   files:
-    - path: output/elprep/test.bam
+    - path: output/elprep/output/test.bam
     - path: output/elprep/versions.yml