nf-core · hyunhwan-jeong · May 14, 2025 · May 14, 2025 · May 14, 2025 · May 20, 2025
diff --git a/modules/nf-core/purgedups/calcuts/meta.yml b/modules/nf-core/purgedups/calcuts/meta.yml
@@ -24,6 +24,7 @@ input:
         type: file
         description: Histogram of coverage
         pattern: "*.stat"
+        ontologies: []
 output:
   - cutoff:
@@ -35,6 +36,7 @@ output:
           type: file
           description: Cutoff file
           pattern: "*.cutoffs"
+          ontologies: []
   - log:
       - meta:
           type: map
@@ -45,11 +47,14 @@ output:
           type: file
           description: Log file
           pattern: ".calcuts.log"
+          ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@mahesh-panchal"
 maintainers:

diff --git a/modules/nf-core/purgedups/calcuts/tests/main.nf.test b/modules/nf-core/purgedups/calcuts/tests/main.nf.test
@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process PURGEDUPS_CALCUTS"
+    script "../main.nf"
+    process "PURGEDUPS_CALCUTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "purgedups"
+    tag "purgedups/pbcstat"
+    tag "purgedups/calcuts"
+
+    test("test_purgedups_calcuts") {
+
+        setup {
+            run("PURGEDUPS_PBCSTAT") {
+                script "../../pbcstat/main.nf"
+
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.paf',checkIfExists:true)
+                        ]
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = PURGEDUPS_PBCSTAT.out.stat
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/purgedups/calcuts/tests/main.nf.test.snap b/modules/nf-core/purgedups/calcuts/tests/main.nf.test.snap
@@ -0,0 +1,51 @@
+{
+    "test_purgedups_calcuts": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cutoffs:md5,e13542222f6e6e4e0d87754956641008"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.calcuts.log:md5,04053f23b4dbb7947e8b2cb820ca6681"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,df5b856012c4a77707e608b2a73f6dde"
+                ],
+                "cutoff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cutoffs:md5,e13542222f6e6e4e0d87754956641008"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.calcuts.log:md5,04053f23b4dbb7947e8b2cb820ca6681"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,df5b856012c4a77707e608b2a73f6dde"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-05-14T14:07:01.617419051"
+    }
+}
diff --git a/modules/nf-core/purgedups/getseqs/meta.yml b/modules/nf-core/purgedups/getseqs/meta.yml
@@ -25,10 +25,12 @@ input:
         type: file
         description: Draft assembly in fasta format
         pattern: "*.fasta"
+        ontologies: []
     - bed:
         type: file
         description: Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS
         pattern: "*.bed"
+        ontologies: []
 output:
   - haplotigs:
       - meta:
@@ -40,6 +42,7 @@ output:
           type: file
           description: Fasta file containing purged haplotigs
           pattern: "*.hap.fa"
+          ontologies: []
   - purged:
       - meta:
           type: map
@@ -50,11 +53,14 @@ output:
           type: file
           description: Fasta file purged of duplicated haplotigs
           pattern: "*.purged.fa"
+          ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@mahesh-panchal"
 maintainers:

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -37,12 +37,6 @@ oncocnv:
 paragraph/idxdepth:
   - modules/nf-core/paragraph/idxdepth/**
   - tests/modules/nf-core/paragraph/idxdepth/**
-purgedups/calcuts:
-  - modules/nf-core/purgedups/calcuts/**
-  - tests/modules/nf-core/purgedups/calcuts/**
-purgedups/getseqs:
-  - modules/nf-core/purgedups/getseqs/**
-  - tests/modules/nf-core/purgedups/getseqs/**
 purgedups/histplot:
   - modules/nf-core/purgedups/histplot/**
   - tests/modules/nf-core/purgedups/histplot/**

diff --git a/tests/modules/nf-core/purgedups/calcuts/main.nf b/tests/modules/nf-core/purgedups/calcuts/main.nf
diff --git a/tests/modules/nf-core/purgedups/calcuts/nextflow.config b/tests/modules/nf-core/purgedups/calcuts/nextflow.config
diff --git a/tests/modules/nf-core/purgedups/calcuts/test.yml b/tests/modules/nf-core/purgedups/calcuts/test.yml
diff --git a/tests/modules/nf-core/purgedups/getseqs/main.nf b/tests/modules/nf-core/purgedups/getseqs/main.nf
diff --git a/tests/modules/nf-core/purgedups/getseqs/nextflow.config b/tests/modules/nf-core/purgedups/getseqs/nextflow.config
diff --git a/tests/modules/nf-core/purgedups/getseqs/test.yml b/tests/modules/nf-core/purgedups/getseqs/test.yml