Merge pull request #115 from kbestak/local-stubs

kbestak · web-flow · commit 9a3b10f42a55 · 2025-04-02T09:32:21.000+02:00
Local stubs
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [PR #115](https://github.com/nf-core/molkart/pull/115) - Added stub section for local modules (@kbestak)
 - [PR #110](https://github.com/nf-core/molkart/pull/110) - Fixed starting index of created crops (0->1) (@miri-2000)
 
 ### Dependencies
diff --git a/modules.json b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "deepcell/mesmer": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     },
                     "ilastik/multicut": {
diff --git a/modules/local/clahe/main.nf b/modules/local/clahe/main.nf
@@ -29,4 +29,15 @@ process CLAHE{
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tiff
+
+        cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_clahe: \$(apply_clahe.dask.py --version)
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/local/createanndata/main.nf b/modules/local/createanndata/main.nf
@@ -29,4 +29,15 @@ process CREATE_ANNDATA {
         molkart_createanndata: \$(create_anndata.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.adata
+
+        cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_createanndata: \$(create_anndata.py --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/createstack/main.nf b/modules/local/createstack/main.nf
@@ -28,4 +28,15 @@ process CREATE_STACK {
         molkart_stack: \$(stack.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.ome.tif
+
+        cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_createanndata: \$(create_anndata.py --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/crophdf5/main.nf b/modules/local/crophdf5/main.nf
@@ -29,4 +29,18 @@ process CROPHDF5 {
         molkart_crophdf5: \$(crop_hdf5.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "Running in stub mode"
+    touch ${prefix}_crop1.hdf5
+    touch ${prefix}_crop2.hdf5
+    touch ${prefix}_CropSummary.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_crophdf5: \$(echo "Stub version")
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/croptiff/main.nf b/modules/local/croptiff/main.nf
@@ -28,4 +28,17 @@ process CROPTIFF {
         molkart_croptiff: \$(crop_tiff.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_stack.ome_crop1.tiff
+    touch ${prefix}_stack.ome_crop2.tiff
+    touch ${prefix}_stack.ome.crop_overview.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_croptiff: \$(crop_tiff.py --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/maskfilter/main.nf b/modules/local/maskfilter/main.nf
@@ -37,6 +37,7 @@ process MASKFILTER {
 
     """
     touch ${prefix}.tif
+    touch ${prefix}.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/spot2cell/main.nf b/modules/local/spot2cell/main.nf
@@ -18,7 +18,6 @@ process SPOT2CELL{
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     spot2cell.py \\
         --spot_table ${spot_table} \\
@@ -31,4 +30,15 @@ process SPOT2CELL{
         molkart_spot2cell: \$(spot2cell.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.csv
+
+        cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_spot2cell: \$(spot2cell.py --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/tiffh5convert/main.nf b/modules/local/tiffh5convert/main.nf
@@ -28,4 +28,15 @@ process TIFFH5CONVERT {
         molkart_crophdf5: \$(crop_hdf5.py --version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.hdf5
+
+        cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_crophdf5: \$(crop_hdf5.py --version)
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/deepcell/mesmer/main.nf b/modules/nf-core/deepcell/mesmer/main.nf
diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test b/modules/nf-core/deepcell/mesmer/tests/main.nf.test
diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test.snap b/modules/nf-core/deepcell/mesmer/tests/main.nf.test.snap
diff --git a/modules/nf-core/deepcell/mesmer/tests/tags.yml b/modules/nf-core/deepcell/mesmer/tests/tags.yml
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -149,4 +149,73 @@ nextflow_pipeline {
             )
         }
     }
+
+    test("Two channels, stardist, mesmer, cellpose, clahe - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/samplesheets/samplesheet_membrane.csv'
+                outdir = "$outputDir"
+                segmentation_method = "cellpose,stardist,mesmer"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_molkart_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Create training subset - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                input = 'https://raw.githubusercontent.com/nf-core/test-datasets/molkart/test_data/samplesheets/samplesheet_membrane.csv'
+                outdir = "$outputDir"
+                create_training_subset = true
+                crop_amount = 2
+                }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_molkart_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
