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Removing ccle_name dependency, adding lua support #88

Merged
merged 23 commits into from
Jan 16, 2025
Merged

Removing ccle_name dependency, adding lua support #88

merged 23 commits into from
Jan 16, 2025

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jdavis3141
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  • ccle_name is no longer necessary and the default cell line columns are now pool_id, depmap_id, & lua
  • ccle_name is added back for portal usage in the adapter script
  • sync_to_s3 now properly formats the inst_info file as tab delimited
  • copies and gzips the EPS_QC output to the sync_to_s3 directory
  • automatically syncs to s3 using build_name
  • removed dependency on log2_n values in various modules

jdavis3141 and others added 23 commits December 18, 2024 09:05
@jdavis3141
- Change default cell_line_cols to include lua, remove ccle_name (gro…
7e09bec 
…ovy)

- Remove ccle_name from cols we get from celldb, add lua
- Change default  cell_line_cols in scripts to match
- Remove deprecated scripts
@jdavis3141
- LUA already named that from cell_line table
3ea3c03
@jdavis3141
- Add LUA to cell_set_and_pool_meta
00a587b
@jdavis3141
- Add LUA to cell_set_and_pool_meta
f312519
@jdavis3141
- Fixed typo in normalize
a909c31
@jdavis3141
- Adding ccle_name back to data in adapter script
bcc107b
@uwidocki
Merge pull request #85 from cmap/main
b4318db 
merging main into this branch with latest updates from main
@uwidocki
added union() to allow variables to be common between cell_line_cols …
1f76488 
…and ctrl_cols, also removed control_mad_sqrtN calculation
@uwidocki
dropped mean_n and control_median_n from compute l2fc module
7b27d78
@uwidocki
removed normalized_n, log2_n from normalization module
72819be
@uwidocki
dropped columns: trt_median_n, trt_mad_sqrtN, trt_MAD_QC, and trt_med…
3b31bd4 
…ian_normalized_n from collapse l2fc module
@uwidocki
brought back trt_median_normalized_n to collapse l2fc module
6f80457
@uwidocki
Merge pull request #86 from cmap/drop_cols
fe9e106 
Drop cols
@jdavis3141
Remove additional dependencies on CCLE_name
0177ad6
@jdavis3141
Merge pull request #87 from cmap/add_lua
9110b36 
Add lua
@jdavis3141
Adding back normalized_n to normalize, unsure why it was removed.
577ed41
@jdavis3141
Add lua to merges in filter_raw_reads
3d28f75
@ashishge1
removed dependency on log2_n
df44aa8 
Now the module needs to accept pseudocount to calculate log2_n on the fly
@jdavis3141
Remove dependency on log2_n from qc_tables
f647366
@jdavis3141
Remove dependency on log2_n from qc_tables
cfcb040
@jdavis3141
Remove dependency on log2_n from qc_tables
6460c3e
@jdavis3141
ensure inst_info is tab delimited
5294c20
@jdavis3141
Merge branch 'main' into testing
973decc
@jdavis3141 jdavis3141 requested review from uwidocki and ashishge1 and removed request for uwidocki and ashishge1 January 16, 2025 00:00
@jdavis3141 jdavis3141 merged commit 31c9fcf into main Jan 16, 2025
@jdavis3141 jdavis3141 deleted the testing branch January 16, 2025 14:44
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3 participants
@jdavis3141 @uwidocki @ashishge1