21th Discussion-1 Nov 2018

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Bioinfo-Core teleconference: Alex Peltzer demo on nexflow and nf-core.

UPDATE: Slide deck can be found here

Link to video coming soon

After the positive feedback from the ISMB workshop, Alex Peltzer has agreed to run a demo for the bioinfo-core on nextflow and nf-core. I plan to schedule this on November 1st, late afternoon in the GMT timezone. Details on how this will occur are being finalised but I would invite everyone to submit any questions ahead of the demo so we can all get the most out of it.

Please add your questions below:

  • How to configure a pipeline for all users
  • How/where is best to store pipelines and make accessible for users
  • How bad are the docker vulnerabilities
  • How to configure dockerised pipelines properly
  • How to convert docker pipelines to singularity (with and without AWS)
  • Easiest pipelines to create from scratch
  • Resources per pipeline language? Such as yaml files for each tool?
  • Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?