feat: refactor code to use Snakemake - #8

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fgvieira wants to merge 15 commits into

mainfrom

Commits on Jul 28, 2026

Convert code from bash to Snakemake
fgvieira
committed
b11e310
Reorganize code
fgvieira
committed
1e1c818

Commits on Jul 29, 2026

Code refactor
fgvieira
committed
9955eb7

Commits on Aug 5, 2026

Fix bcl_convert part
fgvieira
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d5f63b2

Commits on Aug 6, 2026

Small bug fixes
fgvieira
committed
7975fb0

Commits on Aug 10, 2026

More tweaks
fgvieira
committed
1ae2e3e

Commits on Aug 11, 2026

Revert to single SS, and add DAGs
fgvieira
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785a337

Commits on Aug 21, 2026

Several changes
fgvieira
committed
4c0097f

Commits on Aug 24, 2026

Fix issues with workflow rerun and cross-contamination
fgvieira
committed
47be621

Commits on Aug 28, 2026

Update index lists and several tweaks
fgvieira
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77daf62
Fix index check and copy logs
fgvieira
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ea09e1a
Update pixi env
fgvieira
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b17f8a3
Fix index list
fgvieira
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a9f2572
Fix logs
fgvieira
committed
8e6cc1b
Add .gitignore file
fgvieira
committed
c700c1c