nf-core · RobJY · Nov 28, 2023 · Nov 28, 2023 · Nov 28, 2023 · Nov 29, 2023
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test.log
+.nf-test/
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1 +1,4 @@
 repository_type: pipeline
+lint:
+  nextflow_config:
+    - params.input
diff --git a/assets/markers-test.csv b/assets/markers-test.csv
@@ -1,4 +1,4 @@
-channel,cycle,marker_name
+channel_number,cycle_number,marker_name
 1,1,DNA 1
 2,1,Na/K ATPase
 3,1,CD3

diff --git a/assets/markers.csv b/assets/markers.csv
@@ -0,0 +1,13 @@
+channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength
+21,6,DNA_6,DAPI,395,431
+22,6,ELANE,FITC,485,525
+23,6,CD57,Sytox,555,590
+24,6,CD45,Cy5,640,690
+25,7,DNA_7,DAPI,395,431
+26,7,CD11B,FITC,485,525
+27,7,SMA,Sytox,555,590
+28,7,CD16,Cy5,640,690
+29,8,DNA_8,DAPI,395,431
+30,8,ECAD,FITC,485,525
+31,8,FOXP3,Sytox,555,590
+32,8,NCAM,Cy5,640,690
diff --git a/assets/markers_1.csv b/assets/markers_1.csv
@@ -0,0 +1,5 @@
+channel_number,cycle_number,marker_name,filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELANE,FITC,485,525,21
+23,1,CD57,Sytox,555,590,21
+24,1,CD45,Cy5,640,690,21
diff --git a/assets/markers_1_sp.csv b/assets/markers_1_sp.csv
@@ -0,0 +1,5 @@
+channel_number,cycle_number,marker_name,filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELA NE,FITC,485,525,21
+23,1,CD57,Sy tox,555,590,21
+24,1,CD45,Cy5,640,690,21
diff --git a/assets/markers_1_test.csv b/assets/markers_1_test.csv
@@ -0,0 +1,5 @@
+channel_number,cycle_number,marker_name,filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELANE,FITC,485,525,21
+23,1,CD57,Sytox,555,590,21
+24,1,CD45,Cy5,640,690,21
diff --git a/assets/markers_multi_12.csv b/assets/markers_multi_12.csv
@@ -0,0 +1,13 @@
+channel_number,cycle_number,marker_name,filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELANE,FITC,485,525,21
+23,1,CD57,Sytox,555,590,21
+24,2,CD45,Cy5,640,690,21
+25,2,DNA_7,DAPI7,395,431,21
+26,2,ELANE7,FITC7,485,525,21
+27,2,CD577,Sytox7,555,590,21
+28,2,CD457,Cy57,640,690,21
+29,3,DNA_8,DAPI7,395,431,21
+30,3,ELANE8,FITC7,485,525,21
+31,3,CD578,Sytox7,555,590,21
+32,3,CD458,Cy57,640,690,21
diff --git a/assets/markers_multi_6.csv b/assets/markers_multi_6.csv
@@ -0,0 +1,7 @@
+channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELANE,FITC,485,525,21
+23,1,CD57,Sytox,555,590,21
+24,2,CD45,Cy5,640,690,21
+25,2,DNA_7,DAPI7,395,431,21
+26,2,ELANE7,FITC7,485,525,21
diff --git a/assets/markers_multi_8.csv b/assets/markers_multi_8.csv
@@ -0,0 +1,9 @@
+channel_number,cycle_number,marker_name,filter,excitation_wavelength,emission_wavelength,background
+21,1,DNA_6,DAPI,395,431,21
+22,1,ELANE,FITC,485,525,21
+23,1,CD57,Sytox,555,590,21
+24,2,CD45,Cy5,640,690,21
+25,2,DNA_7,DAPI7,395,431,21
+26,2,ELANE7,FITC7,485,525,21
+27,3,CD577,Sytox7,555,590,21
+28,3,CD457,Cy57,640,690,21
diff --git a/assets/nextflow_schema.json b/assets/nextflow_schema.json
@@ -0,0 +1 @@
+../nextflow_schema.json
diff --git a/assets/samplesheet-test.csv b/assets/samplesheet-test.csv
@@ -1,2 +1,2 @@
-sample,data,markerFile,tissue
-TEST1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif,https://raw.githubusercontent.com/jmuhlich/mcmicro/fbe30831fc0f82eeabdca19907e1e90cafb888db/assets/markers-test.csv,tonsil
+sample,cycle_number,channel_count,image_tiles
+TEST1,1,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif
diff --git a/assets/samplesheet_1_row_sample.csv b/assets/samplesheet_1_row_sample.csv
@@ -0,0 +1,2 @@
+sample,image_directory
+TEST1,/home/pollen/HITS/nextflow/test_mcmicro-nf-core/input_sample
diff --git a/assets/samplesheet_1_row_sample_cycle.csv b/assets/samplesheet_1_row_sample_cycle.csv
@@ -0,0 +1,2 @@
+sample,cycle_number,channel_count,image_tiles
+TEST1,1,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif
diff --git a/assets/samplesheet_1_row_sample_cycle_manual.csv b/assets/samplesheet_1_row_sample_cycle_manual.csv
@@ -0,0 +1,2 @@
+sample,cycle_number,channel_count,image_tiles,dfp,ffp
+TEST1,1,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif
diff --git a/assets/samplesheet_1_row_sample_cycle_multi.csv b/assets/samplesheet_1_row_sample_cycle_multi.csv
@@ -0,0 +1,4 @@
+sample,cycle_number,channel_count,image_tiles
+cycif-tonsil,1,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif
+cycif-tonsil,2,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif
+cycif-tonsil,3,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif
diff --git a/assets/samplesheet_1_row_sample_cycle_multi_2.csv b/assets/samplesheet_1_row_sample_cycle_multi_2.csv
@@ -0,0 +1,5 @@
+sample,cycle_number,channel_count,image_tiles
+cycif-tonsil,1,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif
+cycif-tonsil,2,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif
+cycif-tonsil2,2,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif
+cycif-tonsil2,3,10,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif
diff --git a/assets/samplesheet_1_row_sample_manual.csv b/assets/samplesheet_1_row_sample_manual.csv
@@ -0,0 +1,2 @@
+sample,image_directory,dfp,ffp
+TEST1,/home/pollen/HITS/nextflow/test_mcmicro-nf-core/input_sample,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif
diff --git a/assets/samplesheet_1_row_sample_multi.csv b/assets/samplesheet_1_row_sample_multi.csv
@@ -0,0 +1,2 @@
+sample,image_directory,cycle_images
+TEST1,/home/pollen/HITS/nextflow/test_mcmicro-nf-core/input_sample_multi_1,cycif-tonsil-cycle1.ome.tif cycif-tonsil-cycle2.ome.tif
diff --git a/assets/samplesheet_1_row_sample_multi_2.csv b/assets/samplesheet_1_row_sample_multi_2.csv
@@ -0,0 +1,3 @@
+sample,image_directory,cycle_images
+TEST1,/home/pollen/HITS/nextflow/test_mcmicro-nf-core/input_sample_multi_1,cycif-tonsil-cycle1.ome.tif cycif-tonsil-cycle2.ome.tif
+TEST2,/home/pollen/HITS/nextflow/test_mcmicro-nf-core/input_sample_multi_2,cycif-tonsil-cycle3.ome.tif cycif-tonsil-cycle1.ome.tif
diff --git a/assets/schema_input.json b/assets/schema_input.json
diff --git a/assets/schema_input_cycle.json b/assets/schema_input_cycle.json
@@ -0,0 +1,41 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/mcmicro/master/assets/schema_input.json",
+    "title": "nf-core/mcmicro pipeline - params.input_cycle schema",
+    "description": "Schema for the file provided with params.input_cycle",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "sample name must be provided and cannot contain spaces"
+            },
+            "cycle_number": {
+                "type": "integer",
+                "errorMessage": "cycle_number must be provided. It should be 1-based, sequential and have no gaps"
+            },
+            "channel_count": {
+                "type": "integer",
+                "errorMessage": "channel_count name must be provided. It should be 1-based, sequential and have no gaps"
+            },
+            "image_tiles": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Need to provide a path to a directory containing image files"
+            },
+            "dfp": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
+            },
+            "ffp": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
+            }
+        },
+        "required": ["sample","cycle_number","channel_count","image_tiles"]
+    }
+}
diff --git a/assets/schema_input_sample.json b/assets/schema_input_sample.json
@@ -0,0 +1,38 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/mcmicro/master/assets/schema_input.json",
+    "title": "nf-core/mcmicro pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample name must be provided and cannot contain spaces"
+            },
+            "image_directory": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Need to provide a path to a directory containing image files"
+            },
+            "cycle_images": {
+                "type": "string",
+                "pattern": ".*$",
+                "errorMessage": "cycle images for this sample in order"
+            },
+            "dfp": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "provide path to dfp illumination correction file(s) if illumination parameter is manual"
+            },
+            "ffp": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual"
+            }
+        },
+        "required": ["sample","image_directory"]
+    }
+}
diff --git a/assets/schema_marker.json b/assets/schema_marker.json
@@ -0,0 +1,39 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/mcmicro/master/assets/schema_input.json",
+    "title": "nf-core/mcmicro pipeline - params.input schema",
+    "description": "Schema for the file provided with params.marker_sheet",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "channel_number": {
+                "type": "integer",
+                "errorMessage": "channel_number must be provided"
+            },
+            "cycle_number": {
+                "type": "integer",
+                "errorMessage": "cycle_number must be provided"
+            },
+            "marker_name": {
+                "type": "string",
+                "pattern": "\\S",
+                "errorMessage": "marker_name must be provided"
+            },
+            "filter": {
+                "type": "string",
+                "pattern": "\\S",
+                "errorMessage": ""
+            },
+            "excitation_wavelength": {
+                "type": "integer",
+                "errorMessage": ""
+            },
+            "emission_wavelength": {
+                "type": "integer",
+                "errorMessage": ""
+            }
+        },
+        "required": ["channel_number", "cycle_number", "marker_name"]
+    }
+}