Update mygene: topic versions, stub block, sanitizeOutput

modules/nf-core/mygene/main.nf

@@ -13,11 +13,23 @@ process MYGENE {
     output:
     tuple val(meta), path("*.gmt"), emit: gmt
     tuple val(meta), path("*.tsv"), emit: tsv     , optional: true
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions_mygene, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     template "mygene.py"
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gmt
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mygene: \$(python3 -c 'import mygene; print(mygene.__version__)')
+    END_VERSIONS
+    """
 }

modules/nf-core/mygene/meta.yml

@@ -11,9 +11,9 @@ tools:
       documentation: "https://docs.mygene.info/projects/mygene-py/en/latest/"
       tool_dev_url: "https://github.com/biothings/mygene.py"
       doi: "10.1093/nar/gks1114"
-      licence: ["Apache-2.0"]
+      licence:
+        - "Apache-2.0"
       identifier: biotools:mygene
-
 input:
   - - meta:
         type: map
@@ -22,13 +22,13 @@ input:
           e.g. `[ id:'sample1' ]`
     - gene_list:
         type: file
-        description: A tsv/csv file that contains a list of gene ids in one of the columns.
-          By default, the column name should be "gene_id", but this can be changed by
-          using "--columname gene_id" in ext.args.
+        description: A tsv/csv file that contains a list of gene ids in one of the
+          columns. By default, the column name should be "gene_id", but this can
+          be changed by using "--columname gene_id" in ext.args.
         pattern: "*.{csv,tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3752 # CSV
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3752
+          - edam: http://edamontology.org/format_3475
 output:
   gmt:
     - - meta:
@@ -55,14 +55,23 @@ output:
             query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+
+  versions_mygene:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+topics:
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@suzannejin"
 maintainers:

modules/nf-core/mygene/tests/main.nf.test

@@ -25,8 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default options - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - default options - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -49,9 +48,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default with tsv file - gmt") },
-                { assert snapshot(process.out.tsv).match("mygene - default with tsv file - tsv") },
-                { assert snapshot(process.out.versions).match("mygene - default with tsv file - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -74,8 +71,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go category - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go category - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -98,8 +94,29 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go evidence - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go evidence - versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("mygene - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id : 'test'],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv")
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }