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Add qc flags #106

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merged 47 commits into from
Mar 26, 2025
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2daa860
adding plate_cell_qc_flags
jdavis3141 Mar 13, 2025
6201f63
writing out plate_cell_qc_flags
jdavis3141 Mar 13, 2025
a6aa89f
writing out plate_cell_qc_flags
jdavis3141 Mar 13, 2025
9b9f13b
writing out plate_cell_qc_flags
jdavis3141 Mar 13, 2025
6bddb92
ensure skipped wells is not run if the skipped_wells df is not created
jdavis3141 Mar 13, 2025
9d7f026
ensure skipped wells is not run if the skipped_wells df is not created
jdavis3141 Mar 13, 2025
d8c3c50
Ensure median raw count check uses log
jdavis3141 Mar 13, 2025
3adac6c
Reorder functions
jdavis3141 Mar 13, 2025
b60525e
bugfix
jdavis3141 Mar 13, 2025
593c147
- Simplified qc table functionality
jdavis3141 Mar 14, 2025
41f8ee3
-Test creation of default qc params json file
jdavis3141 Mar 14, 2025
133ad24
-Test creation of default qc params json file
jdavis3141 Mar 14, 2025
f2351c3
-Test creation of default qc params json file
jdavis3141 Mar 14, 2025
83b958c
added remaining thresholds
jdavis3141 Mar 14, 2025
ad339ae
adding filtering for fraction of expected controls
jdavis3141 Mar 14, 2025
51f2cd2
bugfix for unused argument.
jdavis3141 Mar 14, 2025
b253bec
non-local outputs need different pattern
jdavis3141 Mar 14, 2025
e546e2c
Updated cellDB_metadata to use new endpoint for pools
jdavis3141 Mar 19, 2025
11a8e86
Update default thresholds for cb_cl_ratio to avoid failing too many s…
jdavis3141 Mar 19, 2025
16f1455
added cell line pass rate summary per plate for portal
ashishge1 Mar 19, 2025
8ac1cd7
Print expected flowcells
jdavis3141 Mar 19, 2025
6034dea
Testing appending critical console outputs to file
jdavis3141 Mar 19, 2025
4cd61c0
Testing appending critical console outputs to file
jdavis3141 Mar 19, 2025
2f98f57
updated default sig and control cols for MTS
ashishge1 Mar 19, 2025
ac5bec3
Testing appending critical console outputs to file
jdavis3141 Mar 19, 2025
0091c1d
Merge remote-tracking branch 'origin/add_qc_flags' into add_qc_flags
jdavis3141 Mar 19, 2025
c9b5aed
Testing appending critical console outputs to file
jdavis3141 Mar 19, 2025
f4ffcca
handling replicate plate
ashishge1 Mar 19, 2025
4e223f4
Merge branch 'add_qc_flags' of https://github.com/cmap/sushi into add…
ashishge1 Mar 19, 2025
97e7982
debugging out not being passed to process in chunks
jdavis3141 Mar 19, 2025
709e094
Merge remote-tracking branch 'origin/add_qc_flags' into add_qc_flags
jdavis3141 Mar 19, 2025
51542a3
debugging out not being passed to process in chunks
jdavis3141 Mar 19, 2025
5ea7f52
debugging out not being passed to process in chunks
jdavis3141 Mar 19, 2025
4b212c9
ensure non-strings can be appended to out critical output
jdavis3141 Mar 19, 2025
8866beb
Adding function to check for na/blank flowcell lanes and names
jdavis3141 Mar 19, 2025
54c0264
Adding functionality to capture na flowcell lanes/names to create_sam…
jdavis3141 Mar 19, 2025
383c83f
Ensure logs subdir is created if necessary when using append_critical…
jdavis3141 Mar 19, 2025
9fbbe62
updated default cb ladder
jdavis3141 Mar 19, 2025
fb74208
fix issue with compute_expected_lines
jdavis3141 Mar 19, 2025
0eece56
adding project code to cell_line_plate_grouping
jdavis3141 Mar 19, 2025
48ca5f4
adding project code to cell_line_plate_grouping
jdavis3141 Mar 19, 2025
48ad143
adding cell_set to default cell_line_cols
jdavis3141 Mar 20, 2025
a00fff6
Fixed over counting bug
yuhjong24 Mar 20, 2025
4c257cb
Added distinct to cellDB meta
yuhjong24 Mar 20, 2025
01735ed
For applying qc flags and filters, use normalized_counts_original.csv…
jdavis3141 Mar 20, 2025
d572086
specify lowercase for barcode ladder
jdavis3141 Mar 25, 2025
67df2ee
Fixed bug in generate_pool_well_qc_table
jdavis3141 Mar 25, 2025
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updated default cb ladder
jdavis3141 committed Mar 19, 2025
commit 9fbbe62247497f1c98721205a39d3e6f10f45dc2
2 changes: 1 addition & 1 deletion scripts/make_config_file.groovy
Original file line number Diff line number Diff line change
@@ -142,7 +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.')

// Additional parameters ordered by when they first appear
string(name: 'BARCODE_COL', defaultValue: 'forward_read_barcode', description: 'Name of the column containing the barcode sequence. The column containing the barcode sequence should have the same name across the Nori output file, the cell line metadata, and the CB metadata. This defaults to \"forward_read_barcode\", and the paramter is first used in COLLATE_FASTQ_READS.')