Skip to content

v0.10.3: update CHANGELOG #53

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ch99l merged 1 commit into from
Oct 5, 2026
Merged

v0.10.3: update CHANGELOG #53

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ This file contains all notable changes to Bambu-Pipe.
- Shortened the polyT right flank for 3' and Visium chemistries (`flexiplex_config.csv`) from 30 T to 9 T, matching the flexiplex presets; ONT reads rarely call the full 30 T homopolymer, so few reads matched the flank during barcode discovery
- Visium samples (`visium-v*`) are now demultiplexed directly against the spot whitelist, as recommended by flexiplex; barcode discovery and flexiplex-filter are skipped, replacing the `-u 0` knee detection workaround
- Updated the supported chemistry names in the README to the official 10x Genomics assay names, with a link to the 10x Genomics long-read compatibility article
- flexiplex flank (`-f`) and barcode (`-e`) edit distances are now set per chemistry in `flexiplex_config.csv` (`flank_max_edit_distance`, `barcode_max_edit_distance`), using the flexiplex preset defaults (`-f 8`, `-e 2`); this replaces the `flexiplex_f_5prime`, `flexiplex_f_3prime` and `flexiplex_e` developer parameters. The previous `-f 13` for 3' and Visium chemistries allowed too many errors for the shortened 9 T flank, causing spurious flank matches that slowed `PREPROCESS_FASTQ` considerably
- Updated the flexiplex flank (`-f`) and barcode (`-e`) edit distances to `-f 8` and `-e 2`, matching the shortened 9 T polyT flank and standardising with the flexiplex documentation; these are now set per chemistry in `flexiplex_config.csv` (`flank_max_edit_distance`, `barcode_max_edit_distance`), replacing the `flexiplex_f_5prime`, `flexiplex_f_3prime` and `flexiplex_e` developer parameters
- Moved the 10x config files out of `assets/10x_config/` into `assets/`, and renamed `adapter_seq_config.csv` to `cutadapt_config.csv` and `flank_seq_config.csv` to `flexiplex_config.csv`

### Removed
Expand Down
Loading