JSON Schema + latest 1.13.1 template

[sk-sahu]

Updates the json schema

PR checklist

• This comment contains a description of changes (with reason)
• Make sure your code lints (nf-core lint .).

[github-actions]

Hi @sk-sahu,

It looks like this pull-request is has been made against the nf-core/scrnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/scrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!

[apeltzer]

Would be great to get some reviews in here ....

[ggabernet]

Looks good to me, just a couple of minor comments and maybe that the Nextflow version should be bumped to 20.10.0 as otherwise there was a problem with the $projectDir variable.

[sk-sahu]

Sure! On it ⌨️

[apeltzer]

Added a tiny bit to the environment.yml to make sure the salmon bit is running through now prperly :-)

[sk-sahu]

@apeltzer I think after changing the environment. It fails with pandoc-citeproc is not available!. I suppose u fixed it already

Loading required package: alevinQC
  Registered S3 method overwritten by 'GGally':
    method from   
    +.gg   ggplot2
  Loading required package: tximport
  Error in .checkPandoc(ignorePandoc) : pandoc-citeproc is not available!
  Calls: alevinQCReport -> .checkPandoc
  Execution halted

[apeltzer]

I wanted to - unfortunately this is a bit provlematic now:

The previous tests were failing because of a known isssue with tbb, which needs to be pinned.

https://github.com/nf-core/scrnaseq/runs/2169179376

Now after I added this, we have a different issue, because pandoc-citeproc fails. I fear we have to update the entire environment once more now ...?

[sk-sahu]

Yeah that's a good idea. Let me update and fix the entire environment

[ggabernet]

Let's see if we can fix the tests with this @sk-sahu

[ggabernet]

Looks good! If the tests pass then from my side ready to go 😄