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Text/workflows dec19 - #26

Merged

poldrack merged 95 commits into

mainfrom

text/workflows-Dec19

Dec 26, 2025

Merged

Text/workflows dec19#26
poldrack merged 95 commits into
mainfrom
text/workflows-Dec19

Commits on Nov 27, 2025
- remove excel section
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- Merge branch 'text/datamgmt-Nov3' into text/workflows-Nov26
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Commits on Nov 28, 2025
- initial section on desiderata
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Commits on Nov 29, 2025
- initial add
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- add summary function
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- add summary function
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- add deps
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- initial add
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Commits on Nov 30, 2025
- working version
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  25ae638
- Add words
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- ruff/blue fixes
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  aaf1818
- fix suffix handling
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  561c3b0
- fix suffix handling
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- working version
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- minor cleanup, format with blue
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Commits on Dec 4, 2025
- initial workflow development
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Commits on Dec 15, 2025
- merge cleanup
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- Merge branch 'main' into text/workflows-Nov26
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- cleanup
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  eb12af0
- update build cmds
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- Merge branch 'main' into text/workflows-Nov26
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Commits on Dec 16, 2025
- add deps
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- Merge branch 'main' into text/workflows-Nov26
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- initial add
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- Merge branch 'main' into text/workflows-Nov26
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- remove 'one of us'
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  98e22ac
Commits on Dec 17, 2025
- add link check
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- full data prep:
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- Merge branch 'main' into text/workflows-Nov26
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Commits on Dec 19, 2025
- add a few topics
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- add deps for scrna-seq example:
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- add deps for scrna-seq example:
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  c0434ca
- initial add
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Commits on Dec 20, 2025
- initial add
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- initial add
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  91d26f8
- formatted and ruffed, about to remove plt.show commands which halt execution
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  925f1f0
Commits on Dec 21, 2025
- add coding prefernces
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- intermediate progress
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  55bfa7f
- add deps
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- add deps
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- final version of monolithic workflow
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- initial add
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- cleanup
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- Add stateless workflow with checkpointing and execution logging
  
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- Fix checkpoint logging to correctly handle interrupts during save
  
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Commits on Dec 22, 2025
- Optimize checkpoint storage and add selective checkpointing
  
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- Fix: Restore layers['counts'] for HVG selection, delete after step 4
  
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- Add steps 9-11 to default checkpoint steps
  
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- Add step 8 (differential expression) to default checkpoint steps
  
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- finished checkpointed workflow section
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- Add Prefect-based workflow with parallel per-cell-type analysis
  
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- Remove parallelization from Prefect workflow to reduce memory usage
  
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  def34e7
- Pin numba<0.63 to fix pynndescent compatibility issue
  
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- Update uv.lock for numba version constraint
  
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- Add execution logging to Prefect workflow
  
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  2154feb
- Disable numba JIT to fix Prefect/pynndescent compatibility
  
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  532a113
- Pre-warm numba before Prefect import to fix JIT compatibility
  
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  8b3a383
- Set NUMBA_CAPTURED_ERRORS=old_style to fix pynndescent print issue
  
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  6f8e524
- set log_prints=False to fix numba issue
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Commits on Dec 23, 2025
- Add Snakemake workflow for scRNA-seq analysis
  
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- Fix feature_name KeyError in Snakemake pseudobulk step
  
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- Handle missing feature_name column in pseudobulk step
  
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- Use step 2 (filtered) checkpoint for var_to_feature mapping
  
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- Add thread specifications to compute-intensive Snakemake rules
  
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- Create output directories in Snakemake scripts
  
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- initial add
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- intermediate progress, full draft of workflow engine intro
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  263bdde
- clean up immutability section
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- initial add
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- Add comprehensive workflow overview documentation
  
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- update deps
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  9461cda
- Extract Prefect workflow params to config file, update output folders
  
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- Add workflow documentation with usage examples
  
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- clean up discussion of engines
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- Add Snakemake report generation for workflow results
  
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- Add simple workflow example for Prefect, Snakemake, and Make
  
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- add reporting cmd
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  2a13fd2
- fix merge conflict
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- fix paths
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  c37360e
- Fix missing doublet UMAP visualization in QC step
  
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  daebf73
- Fix report caption paths in Snakemake rule files
  
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- Fix Snakemake scripts to use named output references
  
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Commits on Dec 24, 2025
- file naming
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- simplify workflow
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- clean up figure
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  066be67
- add return values
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  584e0c1
- first draft of simple workflows
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  7e87b67
- initial add
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- initial add
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  40f8edd
- remove .snakemake before running
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  08ce603
- add expanduser to deal with relative paths
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  bfc5de0
- add log dir and onstart
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  0aee557
- use DATADIR var instead of hard coding
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- add .snakemake
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  3206f8d
- close to a first draft. merging for now, will return to finish later
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  committed
  f7e942c

Commits

Commits on Nov 27, 2025

Commits on Nov 28, 2025

Commits on Nov 29, 2025

Commits on Nov 30, 2025

Commits on Dec 4, 2025

Commits on Dec 15, 2025

Commits on Dec 16, 2025

Commits on Dec 17, 2025

Commits on Dec 19, 2025

Commits on Dec 20, 2025

Commits on Dec 21, 2025

Commits on Dec 22, 2025

Commits on Dec 23, 2025

Commits on Dec 24, 2025