Skip to content
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

Jump to bottom

Make bowtie pre-mapping optional #116

Open
CharlotteAnne opened this issue Jan 28, 2025 · 1 comment
Open

Make bowtie pre-mapping optional #116

CharlotteAnne opened this issue Jan 28, 2025 · 1 comment
Assignees
@slebedeva @CharlotteAnne
Labels
enhancement Improvement for existing functionality

Comments

@CharlotteAnne
Copy link
Contributor

Add flag to rna_align subworkflow to make bowtie premapping optional
flag would need to go in nextflow.config too
@CharlotteAnne CharlotteAnne added the enhancement Improvement for existing functionality label Jan 28, 2025
@CharlotteAnne
Copy link
Contributor Author

One other part of the pipeline that will need changed is the prepare_genome subworkflow - this prepares all the genome inputs like indexes .etc but if you don't do the premapping then the bowtie index doesn't need to be made.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@slebedeva slebedeva

@CharlotteAnne CharlotteAnne

Labels
enhancement Improvement for existing functionality
Projects
None yet
Milestone
No milestone
Development

When branches are created from issues, their pull requests are automatically linked.

refs/heads/116-make-bowtie-pre-mapping-optional nf-core/clipseq
2 participants
@slebedeva @CharlotteAnne