feat(assignment)!: cigar filtering for BWA and optional length filter#273
Open
visze wants to merge 4 commits into
Open
feat(assignment)!: cigar filtering for BWA and optional length filter#273visze wants to merge 4 commits into
visze wants to merge 4 commits into
Conversation
…MAP) User can spcify a regex to filter the CIGAR string in the bam file
…or sequence parameters
…nd consistency
- Updated multiple Snakemake rules to enhance the formatting of shell commands by aligning pipes and parameters for better readability.
- Replaced `&>` with `&>{log}` for consistent logging across rules.
- Ensured proper indentation and spacing in shell commands to follow best practices.
- Added validation requirements in the config schema for sequence collisions to enforce necessary fields when applicable.
Collaborator
Author
|
will close #256 |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
design check sequence collitions needs now start and length. if set with the config af the mapper tool it can use this value.
Also no sequence_length sand alignment start for bbmap is needed anymore.