Add 5-bases Illumina kit support
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 198
- Forks
- 181
- Avg merge
- 6d 17h
- Merged PRs (30d)
- 1
Description
Description of feature
Dear methylseq pipeline developers,
First of all, thank you for maintaining this excellent pipeline.
It would be great if the pipeline could support Bismark 3.x.x, as this version adds support for Illumina's 5-base methylation sequencing chemistry. This would enable methylseq users to analyze data generated with the Illumina 5-base methylation kit without requiring custom modifications, alternative workflows or proprietary software.
Thank you for your work!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating where the methylseq pipeline selects and configures Bismark, then check how the current version is pinned and tested. Confirm what changes are required for Bismark 3.x.x and Illumina 5-base methylation data; done means the pipeline can process that kit without custom workflow changes or proprietary software.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100