nf-test for ashlar (#6931)

* nf-test for ashlar * Update modules/nf-core/ashlar/main.nf Co-authored-by: Simon Pearce <[email protected]> * added multiple tests * pin tifffile version --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Nov 14, 2024 · 7548250 · 7548250
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diff --git a/modules/nf-core/ashlar/environment.yml b/modules/nf-core/ashlar/environment.yml
@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::ashlar=1.18.0
+  - tifffile=2024.1.30
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
@@ -49,4 +49,24 @@ process ASHLAR {
         ashlar: \$(ashlar --version | sed 's/^.*ashlar //' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix        = task.ext.prefix         ?: "${meta.id}"
+    def num_files     = images instanceof List  ? images.size()    : 1
+    def opt_dfp_size  = opt_dfp instanceof List ? opt_dfp.size()   : 1
+    def opt_ffp_size  = opt_ffp instanceof List ? opt_ffp.size()   : 1
+    def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
+    def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
+
+    if ( !dfp_validated ) { error "Please input only zero, one, or N dfp files, where N is the number of input images" }
+    if ( !ffp_validated ) { error "Please input only zero, one, or N ffp files, where N is the number of input images" }
+
+    """
+    touch ${prefix}.ome.tif
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ashlar: \$(ashlar --version | sed 's/^.*ashlar //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/ashlar/tests/main.nf.test b/modules/nf-core/ashlar/tests/main.nf.test
@@ -0,0 +1,155 @@
+nextflow_process {
+
+    name "Test Process ASHLAR"
+    script "../main.nf"
+    process "ASHLAR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ashlar"
+
+    test("ashlar - with fields") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_all' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - 1 cycle - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - all cycles - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif', checkIfExists: true)
+
+                                ]
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - all cycles - with fields - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif', checkIfExists: true)
+
+                                ]
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - with fields - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_all' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/ashlar/tests/main.nf.test.snap b/modules/nf-core/ashlar/tests/main.nf.test.snap
@@ -0,0 +1,167 @@
+{
+    "ashlar - with fields - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-04T13:32:44.241620025"
+    },
+    "ashlar - 1 cycle - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:13:49.614970275"
+    },
+    "ashlar - with fields": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-04T13:28:26.923837754"
+    },
+    "ashlar - all cycles - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:14:14.530220621"
+    },
+    "ashlar - all cycles - with fields - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:14:56.268009236"
+    }
+}
diff --git a/modules/nf-core/ashlar/tests/nextflow.config b/modules/nf-core/ashlar/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: ASHLAR_TILE {
+        ext.args = "--tile-size 512"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -22,9 +22,6 @@ artic/minion:
 ascat:
   - modules/nf-core/ascat/**
   - tests/modules/nf-core/ascat/**
-ashlar:
-  - modules/nf-core/ashlar/**
-  - tests/modules/nf-core/ashlar/**
 ataqv/ataqv:
   - modules/nf-core/ataqv/ataqv/**
   - tests/modules/nf-core/ataqv/ataqv/**