update peddy tests (#5880)

update peddy
nf-core · Jun 25, 2024 · bb8c1e0 · bb8c1e0
1 parent d5b47a2
commit bb8c1e0
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Showing 8 changed files with 135 additions and 51 deletions.
diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf
@@ -35,7 +35,7 @@ process PEDDY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
+        peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' )
     END_VERSIONS
     """
 
@@ -49,6 +49,9 @@ process PEDDY {
     touch ${prefix}.peddy.ped
     touch ${prefix}.html
 
-    touch versions.yml
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' )
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/peddy/tests/main.nf.test b/modules/nf-core/peddy/tests/main.nf.test
@@ -0,0 +1,35 @@
+nextflow_process {
+
+    name "Test Process PEDDY"
+    script "modules/nf-core/peddy/main.nf"
+    process "PEDDY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "peddy"
+
+    test("test - peddy - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz_tbi'], checkIfExists: true)
+                ]
+                input[1] = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/peddy/tests/main.nf.test.snap b/modules/nf-core/peddy/tests/main.nf.test.snap
@@ -0,0 +1,93 @@
+{
+    "test - peddy - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    "versions.yml:md5,d3587e67aded68bcf24c47542efe012f"
+                ],
+                "csv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "ped": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "png": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,d3587e67aded68bcf24c47542efe012f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-25T09:28:05.418978589"
+    }
+}
diff --git a/modules/nf-core/peddy/tests/tags.yml b/modules/nf-core/peddy/tests/tags.yml
@@ -0,0 +1,2 @@
+mosdepth:
+  - "modules/nf-core/peddy/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1197,9 +1197,6 @@ pbbam/pbmerge:
 pbptyper:
   - modules/nf-core/pbptyper/**
   - tests/modules/nf-core/pbptyper/**
-peddy:
-  - modules/nf-core/peddy/**
-  - tests/modules/nf-core/peddy/**
 peka:
   - modules/nf-core/peka/**
   - tests/modules/nf-core/peka/**

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