pangolin - use seqera containers + nf-test; rm pytests

modules/nf-core/pangolin/main.nf

@@ -4,8 +4,8 @@ process PANGOLIN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:4.2--pyhdfd78af_1' :
-        'biocontainers/pangolin:4.2--pyhdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/71/7133e48e32b7baa883b8805e600a143b65316e8a014458b8eb4429eb3596f165/data' :
+        'community.wave.seqera.io/library/pangolin:4.2--3bc97f62c0074e70' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/pangolin/meta.yml

@@ -5,7 +5,7 @@ keywords:
   - pangolin
   - lineage
 tools:
-  - star:
+  - pangolin:
       description: |
         Phylogenetic Assignment of Named Global Outbreak LINeages
       homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
@@ -22,6 +22,10 @@ input:
         description: |
           The genome assembly to be evaluated
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
   - report:
       - meta:
           type: file

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

@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process PANGOLIN"
+    script "../main.nf"
+    process "PANGOLIN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pangolin"
+
+    test("sarscov2 genome [fasta]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pangolin/tests/main.nf.test.snap

@@ -0,0 +1,48 @@
+{
+    "sarscov2 genome [fasta] - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "report": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-06T09:59:41.44254517"
+    },
+    "sarscov2 genome [fasta]": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "report": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-06T09:59:31.881242857"
+    }
+}

tests/config/pytest_modules.yml

@@ -467,9 +467,6 @@ nucmer:
 oncocnv:
   - modules/nf-core/oncocnv/**
   - tests/modules/nf-core/oncocnv/**
-pangolin:
-  - modules/nf-core/pangolin/**
-  - tests/modules/nf-core/pangolin/**
 parabricks/applybqsr:
   - modules/nf-core/parabricks/applybqsr/**
   - tests/modules/nf-core/parabricks/applybqsr/**