21th Discussion-6 Nov 2018

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

UPDATE: Here are the slides from the talk and the full video

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. This will be on November 6th, 3 PM GMT. Details on how this will occur are being finalized 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 the best location to store pipelines and make them accessible for users?
  • How bad are the docker vulnerabilities?
  • How to configure Dockerized pipelines properly?
  • How to convert Docker pipelines to singularity (with and without AWS)?
  • Easiest pipelines to create from scratch
    • What do you mean with that? How would I start writing a pipeline and give advice to a beginner on how to do that?
      • Are there tools, or existing configuration files, that would make the job easier?
      • Any good GUIs such as can be found in Galaxy?
    • Resources per pipeline language? Such as YAML files for each tool?
      • Yes

b Not sure what you mean with this - do you mean how we define dependencies per pipeline?

  • Running the pipeline manager: Once per user? How to enforce port usage? If once per server, how to only use individual users outputs?