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Merge pull request #29 from jmuhlich/sample_sheet_mod
Sample sheet update Thank you to everyone who worked on and discussed this PR!
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@@ -6,3 +6,5 @@ results/ | |
testing/ | ||
testing* | ||
*.pyc | ||
.nf-test.log | ||
.nf-test/ |
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repository_type: pipeline | ||
lint: | ||
nextflow_config: | ||
- params.input |
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channel,cycle,marker_name | ||
channel_number,cycle_number,marker_name | ||
1,1,DNA 1 | ||
2,1,Na/K ATPase | ||
3,1,CD3 | ||
|
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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 |
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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 |
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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 |
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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 |
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@@ -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 |
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@@ -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 |
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sample,image_directory,cycle_images | ||
TEST1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff,cycif-tonsil-cycle1.ome.tif |
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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 |
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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 |
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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 |
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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 |
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sample,image_directory,cycle_images,dfp,ffp | ||
TEST1,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 |
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sample,image_directory,cycle_images | ||
TEST1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff,cycif-tonsil-cycle1.ome.tif;cycif-tonsil-cycle2.ome.tif |
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sample,image_directory,cycle_images | ||
TEST1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff,cycif-tonsil-cycle1.ome.tif;cycif-tonsil-cycle2.ome.tif | ||
TEST2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff,cycif-tonsil-cycle3.ome.tif;cycif-tonsil-cycle1.ome.tif |
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{ | ||
"$schema": "http://json-schema.org/draft-07/schema", | ||
"$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"] | ||
} | ||
} |
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{ | ||
"$schema": "http://json-schema.org/draft-07/schema", | ||
"$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+$", | ||
"errorMessage": "provide path to ffp illumination correction file(s) if illumination parameter is manual" | ||
} | ||
}, | ||
"required": ["sample", "image_directory"] | ||
} | ||
} |
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{ | ||
"$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"] | ||
} | ||
} |
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