New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Tasks as npm modules #78

Open
tiagofilipe12 opened this Issue Aug 25, 2017 · 1 comment

Comments

2 participants
@tiagofilipe12
Member

tiagofilipe12 commented Aug 25, 2017

Tasks could be npm modules and then one could import them as such:

const { join } = require('bionode-watermill')
const samtools = require('watermill-samtools')

const  pipeline = join(stuff, stuff2, samtools)
@thejmazz

This comment has been minimized.

Member

thejmazz commented Aug 25, 2017

Blocked by #75.

First step will be modules within this repo.

Also - we should probably spec out all the responsibilities of a task module by the time we make some of these published:

  • how to do tests for it
  • how to include example files
  • how to include corresponding CWL (see #45)
  • recommend to include examples that fail (e.g. common failures, index file not present)
  • custom logic for that tool (e.g. watch stdout stream and fail task if certain pattern is found - useful for programs that fail but do not give 0 exit code)
  • how the documentation/readme template should be (we want to be consistent across task modules)

@tiagofilipe12 tiagofilipe12 added this to Other in Watermill board Aug 27, 2017

@bmpvieira bmpvieira added this to Backlog in Bionode Project Board Aug 28, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment