Tasks as npm modules
tiagofilipe12 opened this issue · 1 comments
tiagofilipe12 commented
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 commented
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)