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feat: refactor code to use Snakemake #8

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feat: refactor code to use Snakemake #8

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b11e310
Convert code from bash to Snakemake
fgvieira Jul 28, 2026
1e1c818
Reorganize code
fgvieira Jul 28, 2026
9955eb7
Code refactor
fgvieira Jul 29, 2026
d5f63b2
Fix bcl_convert part
fgvieira Aug 5, 2026
7975fb0
Small bug fixes
fgvieira Aug 6, 2026
1ae2e3e
More tweaks
fgvieira Aug 10, 2026
785a337
Revert to single SS, and add DAGs
fgvieira Aug 11, 2026
4c0097f
Several changes
fgvieira Aug 21, 2026
47be621
Fix issues with workflow rerun and cross-contamination
fgvieira Aug 24, 2026
77daf62
Update index lists and several tweaks
fgvieira Aug 28, 2026
ea09e1a
Fix index check and copy logs
fgvieira Aug 28, 2026
b17f8a3
Update pixi env
fgvieira Aug 28, 2026
a9f2572
Fix index list
fgvieira Aug 28, 2026
8e6cc1b
Fix logs
fgvieira Aug 28, 2026
c700c1c
Add .gitignore file
fgvieira Aug 28, 2026
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4 changes: 4 additions & 0 deletions demux/.gitattributes
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Original file line number Diff line number Diff line change
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*.smk linguist-language=Python
Snakefile linguist-language=Python
# SCM syntax highlighting & preventing 3-way merges
pixi.lock merge=binary linguist-language=YAML linguist-generated=true
10 changes: 10 additions & 0 deletions demux/.gitignore
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*~
.*
*__
/cache/
*.bam
*.cram

# pixi environments
.pixi
*.egg-info
291 changes: 0 additions & 291 deletions demux/eDNA_index_list_UDP097-UDP288_UDI001-UDI096_250807.txt
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32 changes: 32 additions & 0 deletions demux/examples/README.md
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# BCL Convert
<details><summary>Rulegraph</summary>

![rulegraph.svg](bcl_convert/rulegraph.svg)
</details>

<details><summary>DAG</summary>

![dag.svg](bcl_convert/dag.svg)
</details>

<details><summary>Filegraph</summary>

![filegraph.svg](bcl_convert/filegraph.svg)
</details>


# Copy (do not re-demultiplex)
<details><summary>Rulegraph</summary>

![rulegraph.svg](copy/rulegraph.svg)
</details>

<details><summary>DAG</summary>

![dag.svg](copy/dag.svg)
</details>

<details><summary>Filegraph</summary>

![filegraph.svg](copy/filegraph.svg)
</details>
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