choose approach for "add your own script" episode

[tobyhodges]

From the lesson development sprint notes:

• several options for this were identified during the lesson development sprint. we should choose one or two to focus on in the tutorial:
  • make script executable and add to path
    • advantage: quick
    • downside:
      • the scripts are not shipped with the CWL document itself
      • not portable to other execution environment without putting the script first
  • pack the scripts into a docker container and make them executable there:
    • advantage: portable
    • downside:
      • only works for people that are using containers
  • use InitialWorkDirRequirement to list script content directly in the CWLToolWrapper
    • example: https://github.com/CompEpigen/ATACseq_workflows/blob/master/CWL/tools/generate_atac_signal_tags.cwl (bad example as here the scripts are too long, only for short scripts)
    • advantage:
      • portable
      • can be used independent of the dependency management solution
    • disadvantage:
      • explodes the complexity of a CWL tool wrapper
      • having to deal with escapes and so on
  • distribute as seperate package via pip / cran / ...

Before working on exercises for this section, we need to choose one or more of these options. @anyone with more CWL experience than I, do you have a suggestion/recommendation?

[skanwal]

Hi @tobyhodges

I would be keen to help with this exercise according to my experience. Also, happy to take inputs from others.

I have mostly taken approach 3 (via InitialWorkDirRequirement) to list script content. If that sounds like a good start, I can start drafting a lesson around it?

[tobyhodges]

Hi @skanwal thanks for reaching out. It's good to hear you're keen to work on this and I encourage you to develop the episode as you describe. There's been some activity on this repository in recent weeks, mostly from @swzCuroverse and @bcosc, so (if you haven't already!) maybe a good idea to get their input and make sure you're all aligned to work towards the same goal

[skanwal]

Thanks @tobyhodges .

I have't had a chance to talk with @swzCuroverse. That's why left a comment at issue#7 to have a quick feedback. Though, I have been following @bcosc work recently on PR.

Happy to have further discussion if needed at any point.