Support different YAML/JSON styles

nextflow-io / cwl2nxf

Import a CWL workflow specification to Nextflow script (experimental)

Apache License 2.0

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Support different YAML/JSON styles #8

Open KevinSayers opened 7 years ago

KevinSayers commented 7 years ago

Currently the converter does not handle the CWL style shown below, only CWL that lacks - id will parse correctly. Also the input file can only be in YAML, JSON is unsupported presently.

- id: fooInput

pditommaso commented 7 years ago

i'm still not understanding if there's an automated conversion/normalisation tool between these two formats. Could you please investigate with the CWL community?

Also create a separate issue for the missing JSON input handling.

KevinSayers commented 7 years ago

There is an automated conversion from YAML to JSON, but all current parsing is based on the references for YAML.

I think we can easily get around this though by checking if

- id: fooID

is present in the lines from a file, and then just doing a replace

cwlline.replace('- id:', '')

pditommaso commented 7 years ago

No, I mean an automated conversion between the different versions of the YAML format.