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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
  • [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
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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
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