Hello I'm new to nf-core pipeline development and I am wondering is there a tool to help modify the default assets/schema_input.json created by nf-core pipelines create for different sample sheet formats, or is that something that is mostly done by hand?

That one is unfortunately by hand at the moment.

nf-core pipeline schema build

only works for

nextflow_schema.json

Okay thanks. Are there some templates for common sample sheets anywhere or best to just look at those from other pipelines?

Other pipelines as there is quite a lot of variation. If you are working in genomics the one in the template is an OK start iirc (handles paired end data for example)

Here are some docs on how to write them: nextflow-io.github.io/nf-schema/latest/nextflow_schema/sample_sheet_schema_specification. They are pretty straightforward so I don't think you will have a lot of issues figuring it out 😛

Fantastic! Thank you

Feel free to ask any questions if you have any 😉