tests: add stub

modules/haplocheck/main.nf

@@ -11,7 +11,7 @@ process HAPLOCHECK {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.txt"), emit: txt
+    tuple val(meta), path("*.txt") , emit: txt
     tuple val(meta), path("*.html"), emit: html
     path "versions.yml"            , emit: versions
 
@@ -29,4 +29,16 @@ process HAPLOCHECK {
         haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch $prefix.txt
+    touch $prefix.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
+    END_VERSIONS
+    """
 }

tests/modules/haplocheck/test.yml

@@ -1,11 +1,20 @@
-- name: "haplocheck"
+- name: haplocheck test_haplocheck
   command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config
   tags:
-    - "haplocheck"
+    - haplocheck
   files:
-    - path: "output/haplocheck/test.html"
+    - path: output/haplocheck/test.html
       md5sum: 59d69052c86edff0301816956eaf4d5f
     - path: output/haplocheck/test.raw.txt
       md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
     - path: output/haplocheck/versions.yml
       md5sum: 94e2fa3ceb3946487319f92cea08c942
+
+- name: haplocheck test_haplocheck using stubs
+  command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config -stub-run
+  tags:
+    - haplocheck
+  files:
+    - path: output/haplocheck/test.html
+    - path: output/haplocheck/test.raw.txt
+    - path: output/haplocheck/versions.yml