Merging template updates and building schema

[skrakau]

Here are the updates for the new nf-core template as well as the changes needed for the new json schema.

I changed the paths in output.md, since the sentence "All paths are relative to the top-level results directory." was added to the template.

Currently there are no full size tests yet, thus the standard test profile is still specified in .github/workflows/awsfulltest.yml (created an issue for this #87).

And I removed the pipeline specific parameters from the "usage.md", since this will be included with the json schema. The help message I didn't touch, since there were no changes in the template for this. I guess the functionality that this can be replaced with the schema will come with future templates or DSL2.

Let me know if I forgot something.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md

[ggabernet]

It looks good to me, after the small corrections 👍

[ggabernet]

Ah wait, linting is failing, there are some markdown issues in output.md and readme.md

[ggabernet]

And I think that nf-core lint is failing cause the input_paths parameter is missing in the json schema

[skrakau]

Yes, sorry, I missed that. Will update

[skrakau]

Although nf-core schema lint . says it's valid (didn't want that parameter there, but then I will add it and hide).

[ggabernet]

yes, that seems like a good solution, to add it but keep it hidden. I can understand that you did not want it there

[skrakau]

OK, I checked the template again, and it seems this parameter doesn't necessarily need to be in nextflow.config, and then maybe it also doesn't need to show up in the schema? Would wait for the test here, but my local linting doesn't fail

[ggabernet]

yes, that should be fine, it was created to use only in the test profile so read paths can be provided there. Don't forget to accept my suggestions though if you agree to them, as they solve a couple of bugs 😄

[skrakau]

Thank you @ggabernet :)

[ggabernet]

sure! 😄