Contributing Guidelines

Bug-fix/Feature process

First of all, please create an issue if not exist already. This will help create the visibility among the team to discuss further.
Always used the dev/devel branch to checkout from for a feature/bug-fix and then create PR against it.

master/main branch is only reserved for stable versions, so it should be only used for release purpose.
Most bug fixes and features should be merged only onto dev. This will be implemented by opening PR reviews against this branch.

Some specifications to make Nextflow pipelines structure standard across the organisation.

Tool/software dependency of a pipeline are handled by combination of conda and docker (env.yml + Dockerfile)
Try to make the tool versions very specific in env.yml file. Ex - samtools==1.12
Try to add test profiles for each of the features making into the pipeline and also make sure they are part of github-actions Continues-Integration (CI) test (.github/ci.yml)
For test profiles it will be needing small datasets, as they quickly need to test in CI. If the dataset is less than few KB keep them under testdata in same repo as pipeline or move them to appropriate places in s3://lifebit-featured-datasets/pipelines/

Checklist -

Version bump in all the places
- In nextflow.config
- In VERSION file
- Change the tag for containers used (should be same with the VERSION file)
Add release note to the changelog.md

NOTE: The docker container with VERSION will be automatically build and pushed to quay.io