Tools: Automatically build CLI help using JSON Schema

[ewels]

Once JSON Schema files are present in pipelines, we can start to use these files to automatically generate the command-line help outputted by pipelines with the --help parameter.

Requires parsing in Groovy in the pipeline code, then writing a function to output nicely formatted text.

[drpatelh]

Assuming this would be similar to the code use in the hlatyping pipeline

[apeltzer]

Yes, but I'd advise to have this as an external small library that can be synced more easily across pipelines :-)

Sarek had/has some script in groovy that are kept externally, to keep these separated from the main.nf - which makes sense I think :-)

[ewels]

Aha yeah - I think this was back from when we started with the custom nf-core metaschema? Looks like we can build on that code for sure though 👍

I'll try to get to this soon, it's basically at the top of my list once I get some more talk slides finished.

[ewels]

Yes, but I'd advise to have this as an external small library that can be synced more easily across pipelines :-)

It would be great to do this generally - see https://github.com/nf-core/tools/issues/634 (will also help / become more relevant with DSL2 file imports).

[drpatelh]

Initial implementation added in https://github.com/nf-core/tools/pull/665

[mashehu]

~As discussed on slack, it would be good to run this function also in the output_documentation step (together with a copyTo for output.md and usage.md) and put the output into a parameters.md, so that every result directory comes bundled with the complete, version specific docs.~

Moved to #741

[drpatelh]

Think we should have a separate issue for this @mashehu as the original proposal has been solved already.

[drpatelh]

However, @ewels mentioned that the code added in #665 , the latest of which is currently sitting in the rnaseq pipeline doesn't factor in some nesting/grouping that is possible to use with the JSON schema?