add stubs for stranger (#1543)

modules/stranger/main.nf

@@ -33,4 +33,15 @@ process STRANGER {
         stranger: \$( stranger --version )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stranger: \$( stranger --version )
+    END_VERSIONS
+    """
 }

tests/modules/stranger/main.nf

@@ -23,3 +23,8 @@ workflow test_stranger_without_optional_variant_catalog {
     EXPANSIONHUNTER ( input, fasta, variant_catalog )
     STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
 }
+
+workflow test_stranger_without_optional_variant_catalog_stubs {
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
+}

tests/modules/stranger/test.yml

@@ -25,3 +25,13 @@
       md5sum: bbe15159195681d5c18596d3ad85c78f
     - path: output/stranger/versions.yml
       md5sum: 8558542a007e90ea5dcdceed3f12585d
+
+- name: stranger test_stranger_without_optional_variant_catalog_stubs
+  command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+    - path: output/expansionhunter/versions.yml
+    - path: output/stranger/test.vcf.gz
+    - path: output/stranger/versions.yml