21th Discussion-6 Nov 2018

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

UPDATE: Here are the slides from the talk Video will be added pending Alex's approval and a suitable server.

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?