This project aims to update the nf-core/phaseimpute pipeline, by adding features and fixing bugs described in the issues page.
Goal
Update the logic and add new features to the pipeline.
Tasks
See below a couple of potential new features to add during the hackathon. Depending on the participation and level of the attendees, more issues could be made available for the hackathon.
Update to topic usage and strict syntax
With the new nextflow linting tool, we aim for 0 errors and 0 warnings.
Level: For anyone interested. Beginners welcome!
Improve documentation
The documentation would need some proof checking !
Level: For anyone interested. Beginners welcome!
Use nf-core/subworkflow
Multiple local subworkflow should be changed to nf-core one. Most of them are already on the nf-core/modules repository.
Level: For people with some experience in Nextflow/nf-core pipelines.
Add QUILT2 imputation
Issue #116
The QUILT software is now available in a new version that would need to be added.
Add sexual chromosome imputation
Issue #31
Update the diploidy information depending on the chromosomal position. Set a parameter to select the start and end of the pseudo-autosomal region.
Level: For people with experience in genomic imputation.
Fix bugs and other issue
There is other issues on github, feel free to check them out or add yours if you encounter any.
