Uses CWL's scatter workflow feature instead of specifying each step explicitly

## Migrated from old repo

CWL gets quite large with 10's inputs, maybe we can try scatter workflow input feature
https://www.commonwl.org/user_guide/23-scatter-workflow/

Things to look out for:

- [ ] how to retrieve file from individual step
- [ ] how to folder each individual step
- [ ] inputs need an array of array. An array of all inputs which are arrays of paired-end reads