Hackathon March 2021

Framework

The wheels of nf-core keep turning thanks to a body of code that we often loosely refer to as "The Framework". This is a bit of a catch-all term that covers anything that isn't a pipeline.

The main projects are the nf-core/tools helper package and the website, though some lines are a little blurred between different repositories (eg. automation tools in pipelines propagated from the helper tools template).

Group members

• Phil Ewels
• Matthias Hörtenhuber
• Lukas Heumos
• Nathan Sheffield
• Gisela Gabernet

nf-core/tools

• [Monday] Collected lots of bugs from people after the last release
  • Now in a v1.13.2 patch fix release milestone
• [Tuesday - Phil]: Fix the template sync (nf-core/tools#911)
• [Tuesday - Phil, Kevin]: more bug fixes and release of v1.13.2
• [Wednesday - Phil, Kevin]: more bug fixes and prep for release ov v.13.3

DSL2 Modules

• [Never happend - Phil]: Write DSL2 module installation versioning (nf-core/tools#868)

Website

• [Mashehu]: add database backend (nf-core/nf-co.re#694):
  • Monday: Running dev version with MySQL and demo site with queries.
  • Tuesday: Got Slack queries running.

PEP Pipeline Schema

• Had a nice discussion about how we could potentially go forward with this

  • Will use nf-core/rnaseq as a test bed
  • Will try to replace validation Python script with some PEP tools
  • Idea is to use PEP to validate sample sheet inputs and print out in a standardised "flat" format. This way we can make use of the more advanced PEP features with very little change to the nf-core pipelines.

• [Nathan] Day 2: Wrote a new package to convert a PEP into customizable outputs for downstream consumption, like a project-level YAML format: https://github.com/pepkit/pepconvert

Refgenie integration

• [Nathan]: Developed a new set of API endpoints to serve unarchived assets via http or s3, getting us a step closer to using refgenie to replace the aws iGenomes files
• [Phil]: Had GitHub issue throughout all 3 days about RefGenie integration but never quite got to starting it