Refgenie Integration (Overview)
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Since Jun 17, 2022.
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Description
Refgenie Integration Overview Issue
This issue is to track the different tasks/issues/PRs related to the integration of Refgenie to nf-core.
Build local Nextflow config with Refgenie paths
- Issue: #1083
- PR: #1090
Status: a working version was implemented in #1090, that relied on newer version of Refgenie that was not yet released at the time. It should be working now with the latest Refgenie version.
Use Refgenie to generate genomes.config file with refgenie genomes
- Issue: #1084
- PR: none
Status: For this part to properly work, all genomes should be available via Refgenie first (see next issue)
Add assets from AWS iGenomes to RefGenie
- Issue: #1086
- PR: https://github.com/refgenie/recipes/pull/1
- PR: https://github.com/refgenie/recipes/pull/2
Status: Not finished, needs to be done by the Refgenie developers.
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