Use --bga when creating bigWigs - #470

Merged

edmundmiller merged 14 commits into

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cursor/fix-issue-in-nf-core-chipseq-4f44

Sep 17, 2025

Commits on Sep 5, 2025

fix: Use --bga in bedtools genomecov for more comprehensive coverage output

cursoragent
authored and
edmundmiller
committed
79f74b7
fix: Move bg to args

edmundmiller
and
pinin4fjords
committed
b54ff62
Change bigWig generation to use -bga for better IGV visualization

cursoragent
authored and
edmundmiller
committed
ba69f7e
chore: nf-core modules install bedtools/genomecov
edmundmiller
committed
801514b
refactor: Replace local bedtools genomecov module with nf-core version
edmundmiller
committed
0d021da
fix: Add robust error handling for flagstat parsing in bedtools genomecov

edmundmiller
and
claude
committed
469ad0d
fix: Improve samtools flagstat stub to generate realistic output

edmundmiller
and
claude
committed
482ceb6
ci: Update summary for CI
edmundmiller
committed
5ec3be7
test: Remove variable HOMER annotation file checksums from snapshots

edmundmiller
and
claude
committed
5ab9267

Commits on Sep 15, 2025

chore: nf-core modules update samtools/flagstat
edmundmiller
committed
b409b59

Commits on Sep 17, 2025