From 53108b6b51d4e968e5b1cc9b07ddb6559cb6d43d Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 9 Aug 2022 15:24:35 +0200
Subject: [PATCH] add stub for qualimap/rnaseq (#1946)

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
---
 modules/qualimap/rnaseq/main.nf | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf
index 3b2f88ad..bd4503b2 100644
--- a/modules/qualimap/rnaseq/main.nf
+++ b/modules/qualimap/rnaseq/main.nf
@@ -20,7 +20,7 @@ process QUALIMAP_RNASEQ {
 
     script:
     def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
+    def prefix   = task.ext.prefix ?: "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     def memory     = task.memory.toGiga() + "G"
 
@@ -49,4 +49,15 @@ process QUALIMAP_RNASEQ {
         qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+    END_VERSIONS
+    """
 }