nf-test for pilon

modules/nf-core/pilon/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
       tool_dev_url: "https://github.com/broadinstitute/pilon"
       doi: "10.1371/journal.pone.0112963"
-      licence: "['GPL v2']"
+      licence: ["GPL-2.0-or-later"]
 input:
   - meta:
       type: map

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

@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process PILON"
+    script "../main.nf"
+    process "PILON"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pilon"
+
+
+    test("Test PILON") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                            ]
+                input[2] = "bam"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pilon/tests/tags.yml

@@ -0,0 +1,2 @@
+pilon:
+  - "modules/nf-core/pilon/**"

tests/config/pytest_modules.yml

@@ -1631,9 +1631,6 @@ picard/sortsam:
 picard/sortvcf:
   - modules/nf-core/picard/sortvcf/**
   - tests/modules/nf-core/picard/sortvcf/**
-pilon:
-  - modules/nf-core/pilon/**
-  - tests/modules/nf-core/pilon/**
 pindel/pindel:
   - modules/nf-core/pindel/pindel/**
   - tests/modules/nf-core/pindel/pindel/**