Refgenie Integration (Overview)

[KevinMenden]

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: RefGenie - build local Nextflow config #1083
• PR: initial working version of refgenie integration #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: Use RefGenie for pipeline template genomes.conf config #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: RefGenie - add assets currently used from AWS-iGenomes #1086
• PR: add bed12 recipe refgenie/recipes#1
• PR: Add attributes mito_name and macs_gsize to fasta asset refgenie/recipes#2

Status: Not finished, needs to be done by the Refgenie developers.