CHORES: Move pytest to nf-test for sratools/prefetch (nf-core#3938)

* move nf_test modules.yml file to .github/

* update and sort file

* use /tmp

* add tests for prefetch

* remove pytest for sratools/prefetch

* Update modules.yml

tests/config/nftest_modules.yml → .github/modules.yml

@@ -3,3 +3,6 @@ fastqc:
 
 snakemake:
   - modules/nf-core/snakemake/**
+
+sratools/prefetch:
+  - modules/nf-core/sratools/prefetch/**

.github/workflows/test.yml

@@ -368,7 +368,7 @@ jobs:
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: "tests/config/nftest_modules.yml"
+          filters: ".github/modules.yml"
           token: "${{ secrets.GITHUB_TOKEN }}"
 
   nf-test:

.gitignore

@@ -1,14 +1,16 @@
+*.code-workspace
+*.pyc
+*.pyo
+.*.sw?
+.DS_Store
 .nextflow*
-work/
-results/
-test_output/
+.nf-test.log
 .nf-test/
-output/
-.DS_Store
-*.code-workspace
-tests/data/
 .screenrc
-.*.sw?
 __pycache__
-*.pyo
-*.pyc
+output/
+results/
+test.xml
+test_output/
+tests/data/
+work/

modules/nf-core/sratools/prefetch/tests/main.nf.test

@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process SRATOOLS_PREFETCH"
+    script "modules/nf-core/sratools/prefetch/main.nf"
+    process "SRATOOLS_PREFETCH"
+    tag "sratools/prefetch"
+    tag "modules_nfcore"
+
+    test("sratools/prefetch") {
+
+        when {
+            params {
+                outdir = "output"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], 'DRR000774' ]
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process).match() }
+            )
+        }
+    }
+
+    test("sratools/prefetch with sralite") {
+
+        when {
+            params {
+                outdir = "output"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], 'SRR1170046' ]
+                input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'])
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process).match() }
+            )
+        }
+    }
+}

modules/nf-core/sratools/prefetch/tests/main.nf.test.snap

@@ -0,0 +1,110 @@
+{
+    "sratools/prefetch with sralite": {
+        "content": [
+            {
+                "stderr": [
+
+                ],
+                "errorReport": null,
+                "exitStatus": 0,
+                "out": {
+                    "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
+                            ]
+                        ]
+                    ],
+                    "1": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ],
+                    "sra": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b"
+                            ]
+                        ]
+                    ],
+                    "versions": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ]
+                },
+                "failed": false,
+                "stdout": [
+
+                ],
+                "errorMessage": null,
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 1,
+                    "tasksSucceeded": 1
+                },
+                "name": "SRATOOLS_PREFETCH",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-10T10:00:01.515299"
+    },
+    "sratools/prefetch": {
+        "content": [
+            {
+                "stderr": [
+
+                ],
+                "errorReport": null,
+                "exitStatus": 0,
+                "out": {
+                    "0": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
+                            ]
+                        ]
+                    ],
+                    "1": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ],
+                    "sra": [
+                        [
+                            {
+                                "id": "test",
+                                "single_end": false
+                            },
+                            [
+                                "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0"
+                            ]
+                        ]
+                    ],
+                    "versions": [
+                        "versions.yml:md5,c967dea4135cb75490e1e801c4639efc"
+                    ]
+                },
+                "failed": false,
+                "stdout": [
+
+                ],
+                "errorMessage": null,
+                "trace": {
+                    "tasksFailed": 0,
+                    "tasksCount": 1,
+                    "tasksSucceeded": 1
+                },
+                "name": "SRATOOLS_PREFETCH",
+                "success": true
+            }
+        ],
+        "timestamp": "2023-10-10T09:58:01.781848"
+    }
+}

nf-test.config

@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir "/tmp"
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/config/nf-test.config"

tests/config/pytest_modules.yml

@@ -3712,10 +3712,6 @@ sratools/fasterqdump:
   - modules/nf-core/sratools/fasterqdump/**
   - tests/modules/nf-core/sratools/fasterqdump/**
 
-sratools/prefetch:
-  - modules/nf-core/sratools/prefetch/**
-  - tests/modules/nf-core/sratools/prefetch/**
-
 srst2/srst2:
   - modules/nf-core/srst2/srst2/**
   - tests/modules/nf-core/srst2/srst2/**