Add qc flags #106
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Add qc flags #106
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jdavis3141
commented
Mar 17, 2025
jdavis3141
commented
- Finalizing qc_flags functionality
- Writes out tables and flag tables for each qc level
- Includes the option to filter samples that fail qc flags (at normalized_counts)
- Some reformatting
added it to control cols defaults and renamed it in sample meta.
…_output Move console log into logs subdir
uwidocki
requested changes
Mar 20, 2025
| @@ -125,7 +142,7 @@ pipeline { | |||
| string(name: 'SAMPLE_META', defaultValue: 'sample_meta.csv', description: 'File name in BUILD_DIR of the sample meta.') | |||
| string(name: 'CELL_SET_AND_POOL_META', defaultValue: 'cell_set_and_pool_meta.csv', description: 'Cell set and pool information for this run.') | |||
| string(name: 'CELL_LINE_META', defaultValue: 'cell_line_meta.csv', description: 'File in BUILD_DIR containing cell line metadata') | |||
| string(name: 'CONTROL_BARCODE_META', defaultValue: 'h-b', description: 'Metadata for control barcodes. If the CBs exist in cellDB, this can simply be the cb_ladder name (ie, h-a). Otherwise, this must be a csv file located in the build directory.') | |||
| string(name: 'CONTROL_BARCODE_META', defaultValue: 'h-a', description: 'Metadata for control barcodes. If the CBs exist in cellDB, this can simply be the cb_ladder name (ie, h-a). Otherwise, this must be a csv file located in the build directory.') | |||
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should we specify that the string needs to be all lowercase, too since some people write it as "H-a"?
Added extra condition so that contaminants are not counted as recovered cell lines
yuhjong24
approved these changes
Mar 20, 2025
… if it exists to prevent issues with re-runs
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