Comments (1)
When we do this components should have a short blurb providing information and needed citation's. Actually the citation would be a good field to add to the component and as many pipeline's may not be accepted for publication my recommendation is to submit them all to an appropriate journal (such as biRxiv) which accepts but doesn't publish and then we can use these as citation sources
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Related Issues (20)
- create a docker for bifrost launcher HOT 1
- Fix setup to install indexes for DB and species install.
- Change it so components can be re-installed onto themselves (for development adjustments to config.yaml) as deleting from DB to update is less than ideal.
- Clean up setup folder. shouldnt be needed but currently dockerfiles in others are pulling common resources from it. Should move those into the components (or base)
- Columns can be added/hidden by the user
- Download finders result for selected samples as csv
- Add input species for components with a species requirement. This is so if the user changes the species the component still has info on which species it ran against
- Update bifrostlib for samplecomponents to reflect schema2.0 and beyond, right now its more hardcoded for snakemake purposes
- Update tests with new bifrostlib functionality
- Split tests into fast and slow (or unit/integration) so that the watchdog runs quick ones first and then bigger ones after for faster feedback loops
- Fix issue where a component requirement isn't working. Currently it's checking off it's own id and not that of the target.
- push newest bifrostlib to all components
- turn bifrost into bifrostlib submodule and reporter submodule so that bifrost is just the collection and documentation organization
- Create version tag for all components and check dockerhub (update github actions)that it reflects properly HOT 1
- Adjust sample_component path to include final path not just sample path
- Fix for bifrost_run_launcher test will affect other tests as calling run_program isn't neccesary or desired now
- Requirements not passed failing the component
- QC score HOT 4
- chewBBACA component for Bifrost HOT 4
- Documentation link at readme.md yields a 404
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