putting alessio's test since those are nextflow based

cbcrg · Oct 16, 2024 · 0ba06ba · 0ba06ba
1 parent 125721a
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diff --git a/tests/handle_data.nf.test b/tests/handle_data.nf.test
@@ -0,0 +1,34 @@
+
+nextflow_workflow {
+
+    name "Test Workflow HANDLE_DATA"
+    script "../workflows/handle_data.nf"
+    workflow "HANDLE_DATA"
+
+    test("Test reproducibility of data handling") {
+
+        when {
+
+            // make so that nf-test will see a singularity cache dir where is usally set to, again interpretation of projectdir has to be done here and not rely on an external config.
+            params {
+                singularity_cache_dir = "${projectDir}/singularity_cache"
+            }
+
+            // repeating in input[0-1] the same content of params.csv and parma.exp_conf present in the test.config because nf-test does not interpret the ${projectDir} correctly otherwise
+            workflow {
+                """
+                input[0] = "${projectDir}/bin/tests/test_data/dna_experiment/test_with_split.csv"
+                input[1] = "${projectDir}/examples/test.json"
+                input[2] = Channel.of("TESTING")
+                """
+            }
+        }
+
+        then {
+
+            assert workflow.success
+
+            assert snapshot(workflow.out.data).match()
+        }
+    }
+}
diff --git a/tests/handle_data.nf.test.snap b/tests/handle_data.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "Test reproducibility of data handling": {
+        "content": [
+            [
+                [
+                    "test_with_split.csv - shuffle",
+                    "no_split",
+                    "test_with_split-shuffled-experiment.json:md5,04768aaf767c8cd2c043f510432b78e0",
+                    "test_with_split-shuffle.csv:md5,b69d4616b7cecaa62d5e3e41c010d7c4"
+                ],
+                [
+                    "test_with_split.csv - test-1",
+                    "no_split",
+                    "test-1-experiment.json:md5,4ce80948f2bd82af2ca42e3bb81fbb32",
+                    "test_with_split-test-1-trans.csv:md5,8dbc69f2845da31ff8ab2381a2667a4e"
+                ],
+                [
+                    "test_with_split.csv - test-2",
+                    "RandomSplitter_0.34_0.33_0.33_4",
+                    "test-2-experiment.json:md5,5bb998041e683c327dcfec81a908fa36",
+                    "test_with_split-test-2-trans.csv:md5,64ecd933e2bc0c0d2c42a107288c3a0e"
+                ],
+                [
+                    "test_with_split.csv - test-3",
+                    "no_split",
+                    "test-3-experiment.json:md5,2a6576e2eee24cbd026e3db7944d2733",
+                    "test_with_split-test-3-trans.csv:md5,9f0179b00db4bd806df0d0760e036020"
+                ],
+                [
+                    "test_with_split.csv - test-4",
+                    "RandomSplitter_0.34_0.33_0.33_4",
+                    "test-4-experiment.json:md5,888b5a8cdf10c3f6fbd0c061c127b28b",
+                    "test_with_split-test-4-trans.csv:md5,35c600e3d5af5280c3ce50e683d4e1da"
+                ],
+                [
+                    "test_with_split.csv - test-5",
+                    "no_split",
+                    "test-5-experiment.json:md5,0dd70a06361d79438e1cd154cacf132b",
+                    "test_with_split-test-5-trans.csv:md5,535ede6479723133ff71020eec9de4b1"
+                ],
+                [
+                    "test_with_split.csv - test-6",
+                    "RandomSplitter_0.34_0.33_0.33_4",
+                    "test-6-experiment.json:md5,fde920c7e4d815a56e4825dfd3f7e415",
+                    "test_with_split-test-6-trans.csv:md5,fbbdfd06c6ec07b126ae68592bd09e54"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-12T17:34:58.30196"
+    }
+}
diff --git a/tests/handle_tune.nf.test b/tests/handle_tune.nf.test
@@ -0,0 +1,58 @@
+nextflow_workflow {
+
+    name "Test Workflow HANDLE_TUNE"
+    script "../workflows/handle_tune.nf"
+    workflow "HANDLE_TUNE"
+
+    test("Test reproducibility of model tuning") {
+
+        setup {
+            run("HANDLE_DATA") {
+                script "../workflows/handle_data.nf"
+                workflow {
+                    """
+                    input[0] = "${projectDir}/bin/tests/test_data/dna_experiment/test_with_split.csv"
+                    input[1] = "${projectDir}/examples/test.json"
+                    input[2] = Channel.of("TESTING")
+                    """
+                }
+            }
+        }
+
+        when {
+
+            // make so that nf-test will see a singularity cache dir where is usally set to, again interpretation of projectdir has to be done here and not rely on an external config.
+            params {
+                singularity_cache_dir = "${projectDir}/singularity_cache"
+                debug_mode = true
+
+
+                max_gpus = 0
+
+
+            }
+
+            // repeating in input[0-1] the same content params.model of params.tune_conf present in the test.config because nf-test does not interpret the ${projectDir} correctly otherwise
+            // using both only CPU and only GPU.
+            workflow {
+                """
+                input[0] = "${projectDir}/bin/tests/test_model/dnatofloat_model.py"
+                input[1] = "${projectDir}/bin/tests/test_model/dnatofloat_model_cpu.yaml"
+                input[2] = HANDLE_DATA.out.data
+                """
+            }
+        }
+
+        then {
+
+            // first chech that the model initialization is always identical
+            // then check that the seeds used are the same through randomly picked numbers
+            assertAll(
+            { assert workflow.success }, 
+            { assert snapshot(workflow.out.debug).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/tests/handle_tune.nf.test.snap b/tests/handle_tune.nf.test.snap
@@ -0,0 +1,134 @@
+{
+    "Test reproducibility of model tuning": {
+        "content": [
+            [
+                [
+                    [
+                        "debug_test_with_split-test-6",
+                        [
+                            "best_model_seed.txt:md5,24b16fede9a67c9251d3e7c7161c83ac",
+                            "best_model_val_pred.txt:md5,08f6d202085b428fa0add4f36084fa59"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-test-5",
+                        [
+                            "best_model_seed.txt:md5,24b16fede9a67c9251d3e7c7161c83ac",
+                            "best_model_val_pred.txt:md5,03b1529fca6d3e337a2debe494ab4ef5"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-test-4",
+                        [
+                            "best_model_seed.txt:md5,4c56ff4ce4aaf9573aa5dff913df997a",
+                            "best_model_val_pred.txt:md5,f9e0e0a84270d98fd9605c32c8feb3ab"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-test-3",
+                        [
+                            "best_model_seed.txt:md5,4c56ff4ce4aaf9573aa5dff913df997a",
+                            "best_model_val_pred.txt:md5,7d83395ef9592300c062666031141443"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-test-2",
+                        [
+                            "best_model_seed.txt:md5,4c56ff4ce4aaf9573aa5dff913df997a",
+                            "best_model_val_pred.txt:md5,f9e0e0a84270d98fd9605c32c8feb3ab"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-test-1",
+                        [
+                            "best_model_seed.txt:md5,4c56ff4ce4aaf9573aa5dff913df997a",
+                            "best_model_val_pred.txt:md5,7d83395ef9592300c062666031141443"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ],
+                    [
+                        "debug_test_with_split-shuffle",
+                        [
+                            "best_model_seed.txt:md5,4c56ff4ce4aaf9573aa5dff913df997a",
+                            "best_model_val_pred.txt:md5,d151f5cedafe154617ea3e05826261af"
+                        ],
+                        [
+                            "model.pt:md5,d4adc1515585c66c2843ecdace31de15",
+                            "model.pt:md5,e1310d3caaa760554d47074742fe8359",
+                            "model.pt:md5,8a5d5ada2f493eb23508ec423c500d1b"
+                        ],
+                        [
+                            "seeds.txt:md5,ccae8b777d84a1d4ee9dc8965a4d8bd3",
+                            "seeds.txt:md5,4cee7381be8890309148bc2af7ab50c3",
+                            "seeds.txt:md5,6e77a0e21f32c2a9f9a0e27eee59c336"
+                        ]
+                    ]
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-07-18T19:08:19.490204"
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -0,0 +1,36 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+/*
+params {
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+
+    // Base directory for nf-core/fetchngs test data
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
+}
+
+
+// Impose sensible resource limits for testing
+process {
+    withName: '.*' {
+        cpus   = 2
+        memory = 3.GB
+        time   = 2.h
+    }
+}
+*/
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }