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Tasks as npm modules #78

tiagofilipe12 opened this issue Aug 25, 2017 · 1 comment

Tasks as npm modules #78

tiagofilipe12 opened this issue Aug 25, 2017 · 1 comment


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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)
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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 Common Workflow Language (CWL) support? #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
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