Changes to tackle revision for hotfix 1.0.1

CHANGELOG.md

@@ -10,6 +10,8 @@ Hotfix to tackle some bugs
 ### `Added`
 
 - Template update for nf-core/tools version 4.0.3
+- Adding new conf/tests folder
+- Adding new test for coordinate mode to check the bugfixes
 
 ### `Fixed`
 

subworkflows/local/baysor_run_prior_segmentation_mask/main.nf

@@ -4,7 +4,7 @@
 
 include { BAYSOR_PREPROCESS_TRANSCRIPTS    } from '../../../modules/local/baysor/preprocess/main'
 include { BAYSOR_RUN                       } from '../../../modules/local/baysor/run/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 
 workflow BAYSOR_RUN_PRIOR_SEGMENTATION_MASK {

subworkflows/local/baysor_run_transcripts_parquet/main.nf

@@ -15,7 +15,7 @@ include { BAYSOR_RUN                       } from '../../../modules/local/baysor
 include { BAYSOR_PREPROCESS_TRANSCRIPTS    } from '../../../modules/local/baysor/preprocess/main'
 include { XENIUM_PATCH_STITCH              } from '../../../modules/local/xenium_patch/stitch/main'
 include { RECONSTRUCT_PATCHES              } from '../../../modules/local/utility/reconstruct_patches/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 
 workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {

subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf

@@ -6,7 +6,7 @@ include { XENIUM_PATCH_DIVIDE              } from '../../../modules/local/xenium
 include { BAYSOR_PREPROCESS_TRANSCRIPTS    } from '../../../modules/local/baysor/preprocess/main'
 include { BAYSOR_RUN                       } from '../../../modules/local/baysor/run/main'
 include { XENIUM_PATCH_STITCH              } from '../../../modules/local/xenium_patch/stitch/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET_TILED {
 

subworkflows/local/cellpose_baysor_import_segmentation/main.nf

@@ -11,7 +11,7 @@ include { CONVERT_MASK_UINT32              } from '../../../modules/local/utilit
 include { BAYSOR_PREPROCESS_TRANSCRIPTS    } from '../../../modules/local/baysor/preprocess/main'
 include { RESIZE_TIF                       } from '../../../modules/local/utility/resize_tif/main'
 include { GET_TRANSCRIPTS_COORDINATES      } from '../../../modules/local/utility/get_coordinates/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
     take:

subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf

@@ -9,7 +9,7 @@ include { CELLPOSE as CELLPOSE_CELLS       } from '../../../modules/nf-core/cell
 include { EXTRACT_DAPI                     } from '../../../modules/local/utility/extract_dapi/main'
 include { STARDIST as STARDIST_NUCLEI      } from '../../../modules/nf-core/stardist/main'
 include { CONVERT_MASK_UINT32              } from '../../../modules/local/utility/convert_mask_uint32/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
     take:

subworkflows/local/proseg_preset_proseg2baysor/main.nf

@@ -4,7 +4,7 @@
 
 include { PROSEG                           } from '../../../modules/local/proseg/preset/main'
 include { PROSEG2BAYSOR                    } from '../../../modules/local/proseg/proseg2baysor/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow PROSEG_PRESET_PROSEG2BAYSOR {
     take:

subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf

@@ -6,7 +6,7 @@ include { XENIUM_PATCH_DIVIDE              } from '../../../modules/local/xenium
 include { PROSEG                           } from '../../../modules/local/proseg/preset/main'
 include { PROSEG2BAYSOR                    } from '../../../modules/local/proseg/proseg2baysor/main'
 include { XENIUM_PATCH_STITCH              } from '../../../modules/local/xenium_patch/stitch/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow PROSEG_PRESET_PROSEG2BAYSOR_TILED {
 

subworkflows/local/segger_create_train_predict/main.nf

@@ -6,7 +6,7 @@ include { SEGGER2XR                        } from '../../../modules/local/utilit
 include { SEGGER_TRAIN                     } from '../../../modules/local/segger/train/main'
 include { SEGGER_PREDICT                   } from '../../../modules/local/segger/predict/main'
 include { SEGGER_CREATE_DATASET            } from '../../../modules/local/segger/create_dataset/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow SEGGER_CREATE_TRAIN_PREDICT {
     take:

subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf

@@ -6,7 +6,7 @@ include { RESOLIFT                         } from '../../../modules/local/resoli
 include { EXTRACT_DAPI                     } from '../../../modules/local/utility/extract_dapi/main'
 include { STARDIST as STARDIST_NUCLEI      } from '../../../modules/nf-core/stardist/main'
 include { CONVERT_MASK_UINT32              } from '../../../modules/local/utility/convert_mask_uint32/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow STARDIST_RESOLIFT_MORPHOLOGY_OME_TIF {
     take:

subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf

@@ -3,7 +3,7 @@
 //
 
 include { XENIUMRANGER_RESEGMENT           } from '../../../modules/nf-core/xeniumranger/resegment/main'
-include { XENIUMRANGER_IMPORTSEGMENTATION } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
+include { XENIUMRANGER_IMPORTSEGMENTATION  } from '../../../modules/nf-core/xeniumranger/importsegmentation/main'
 
 workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
     take:

tests/.nftignore

@@ -10,3 +10,43 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 **/proseg/preset/**
+
+# proseg2baysor re-serializes proseg's segmentation non-deterministically (geojson/csv);
+# this propagates into every spatialdata bundle built from it
+coordinate/proseg/proseg2baysor/test_run/cell-polygons.geojson
+coordinate/proseg/proseg2baysor/test_run/transcript-metadata.csv
+coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/points/**
+coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/shapes/**
+coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/tables/**
+coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/points/**
+coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/shapes/**
+coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/tables/**
+coordinate/spatialdata/meta/spatialdata/test_run/metadata/points/**
+coordinate/spatialdata/meta/spatialdata/test_run/metadata/shapes/**
+coordinate/spatialdata/meta/spatialdata/test_run/metadata/tables/**
+
+# xeniumranger's internal secondary analysis (clustering/PCA/UMAP/diffexp) and
+# resegmentation are not run-to-run reproducible; only existence is checked
+xeniumranger/test_run/**
+coordinate/untar/test_run/**
+coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/points/**
+coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/shapes/**
+coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/tables/**
+
+# MultiQC pre/post-Xeniumranger reports embed non-deterministic run data
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report.html
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report_data/llms-full.txt
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report_data/multiqc.log
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report_data/multiqc.parquet
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report_data/multiqc_data.json
+coordinate/multiqc/*/MultiQC-*-Xeniumranger-import-segmentation-Run_multiqc_report_data/multiqc_sources.txt
+
+# OME-Zarr group metadata (member/channel ordering) is not written in a stable
+# order across runs, both for the images subgroup and for each bundle's root
+# store (which declares its images/points/shapes/tables members); the
+# underlying pixel/array chunk data itself is unaffected
+**/images/zarr.json
+coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/zarr.json
+coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/zarr.json
+coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/zarr.json
+coordinate/spatialdata/meta/spatialdata/test_run/metadata/zarr.json

tests/coordinate_mode.nf.test

@@ -3,7 +3,55 @@ nextflow_pipeline {
     name "Test pipeline for the `coordinate` mode, test run the proseg subworkflow"
     script "../main.nf"
     tag "pipeline"
-    config "../conf/test_coordinate_mode.config"
+    config "../conf/tests/test_coordinate_mode.config"
+
+
+    test("-profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // Stable_name: All files + folders in ${params.outdir}/ with a stable name.
+            // Zarr tables store one chunk file per obs/var column, leading to incoherent output files.
+            // Only the tables' existence is checked below instead.
+            // Xeniumranger's secondary analysis is skipped entirely on some runs (writing
+            // a single note.txt instead of the clustering/diffexp/pca/umap tree).
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: [
+                'pipeline_info/*.{html,json,txt}',
+                '**/proseg/preset/**',
+                'coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/tables/**',
+                'coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/tables/**',
+                'coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/tables/**',
+                'coordinate/spatialdata/meta/spatialdata/test_run/metadata/tables/**',
+                'xeniumranger/test_run/**',
+                'coordinate/untar/test_run/**',
+            ])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_spatialaxe_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() },
+                { assert file("$outputDir/coordinate/proseg/preset/test_run/proseg-output.zarr").exists() },
+                { assert file("$outputDir/coordinate/spatialdata/write/spatialdata/test_run/raw_bundle/tables/table").exists() },
+                { assert file("$outputDir/coordinate/spatialdata/write/spatialdata/test_run/redefined_bundle/tables/table").exists() },
+                { assert file("$outputDir/coordinate/spatialdata/merge/spatialdata/test_run/merged_bundle/tables/raw_table").exists() },
+                { assert file("$outputDir/coordinate/spatialdata/meta/spatialdata/test_run/metadata/tables/raw_table").exists() },
+                { assert file("$outputDir/xeniumranger/test_run").exists() },
+                { assert file("$outputDir/coordinate/untar/test_run").exists() },
+            )
+        }
+    }
 
     test("-profile test stub") {