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Seperate ends #57

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merged 27 commits into from
Jan 13, 2025
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010d9d1
feat: vscode ignore stashes
rroutsong Dec 10, 2024
ef9f39c
fix: seperate paired and single end rules, conditional import
rroutsong Dec 10, 2024
01bd7d5
Merge branch 'seperate_ends' of http://github.com/OpenOmics/chrom-see…
rroutsong Dec 10, 2024
11bd817
fix: add back trim-align-dedup ended rules
rroutsong Dec 10, 2024
c3a12ca
fix: changeset from testing with blocked toy dataset
rroutsong Dec 10, 2024
9735b6e
fix: testing fixes with the 3 toy datasets
rroutsong Dec 10, 2024
05d7fa0
fix: add missing import to single end qc rules
rroutsong Dec 10, 2024
e3da83c
fix: correct ci dry run failures
rroutsong Dec 11, 2024
8ea4e6c
fix: remove file_stems
rroutsong Dec 11, 2024
ef4a33c
fix: add conditional when no inputs
rroutsong Dec 11, 2024
83bb23c
fix: null output on just paired end
rroutsong Dec 11, 2024
b515b64
fix: prettify rule put option arg at end with no line break
rroutsong Dec 11, 2024
5d9cd55
fix: lint
rroutsong Dec 23, 2024
63489b2
fix: lint
rroutsong Dec 23, 2024
27709bd
fix: correctly route insert size metric files at rule all level
rroutsong Dec 27, 2024
4b32239
fix: reroute insert size metrics and RPGC bigwigs
rroutsong Dec 27, 2024
c8e2b06
fix: review suggestions
rroutsong Dec 30, 2024
f3bf548
fix: update bam2bw paired end execution
rroutsong Dec 30, 2024
5d05803
fix: ppqt routing and acceptance of tagalign
rroutsong Jan 2, 2025
ddbafc9
fix: correct some parameters of ppqt tagalign and ppqt
rroutsong Jan 3, 2025
e990890
fix: move to 44371755 and lint
rroutsong Jan 6, 2025
a3bc8e0
fix: move to 44371755 and lint
rroutsong Jan 6, 2025
c1b9441
fix: continued move to and linting
rroutsong Jan 6, 2025
3f8826e
fix: correct ppqt_tagalign functionality
rroutsong Jan 6, 2025
de2fc0b
fix: review changes
rroutsong Jan 10, 2025
3e19dbd
fix: revert ppqt wildcard removal
rroutsong Jan 10, 2025
33040a2
feat: add ppqt fragment length file
rroutsong Jan 10, 2025
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3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,9 @@ __pycache__/
*.py[cod]
*$py.class

# VSCode
*~Stashed changes

# C extensions
*.so

Expand Down
Empty file modified bin/DiffBind_v2_Deseq2_block.Rmd
100644 → 100755
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Empty file modified bin/DiffBind_v2_EdgeR.Rmd
100644 → 100755
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Empty file modified bin/DiffBind_v2_EdgeR_block.Rmd
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