From 58d4dec70be5ac5eb2356aac351593c27f77502a Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Tue, 3 May 2022 11:09:54 +0200
Subject: [PATCH] Update samtools view

---
 modules.json                                  |  2 +-
 modules/nf-core/modules/samtools/view/main.nf | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 071234d..b568d9c 100644
--- a/modules.json
+++ b/modules.json
@@ -73,7 +73,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/view": {
-                "git_sha": "12afb6b0faf3cabf769c9a2a7dd477e3f066eac0"
+                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
             },
             "untar": {
                 "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf
index 11cfb74..55194e8 100644
--- a/modules/nf-core/modules/samtools/view/main.nf
+++ b/modules/nf-core/modules/samtools/view/main.nf
@@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }