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nf-core

Hello!
Quick question: Does `purple` output `.tbi` files for the `.vcf.gz` files?
My colleague ran a test case and the index files are present, but when I run a stub run they are missing. There doesn't seem to be any mention of the index files in the <https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md#vcf|documentation> either.
I'm wondering if this is a bug in the stub behaviour of the `purple` module in `onoanalyser`. :thinking_face:

Created issue: <https://github.com/nf-core/oncoanalyser/issues/301|github.com/nf-core/oncoanalyser/issues/301>

Hi Beatriz, thanks for creating the issue ! We'll look into it and get back to you :slightly_smiling_face:

Thank you!
I have opened a PR to fix this - see  <https://github.com/nf-core/oncoanalyser/pull/303|github.com/nf-core/oncoanalyser/pull/303> - since this bug blocks the development of our pipeline.
But it is failing on linting and nf-test due a syntax bug somewhere else in the code base (I heard you are already working to migrate to strict syntax). Also, I am not sure about the structure of the changelog and couldn't find any contributing information about it.
Could you help me out with this?

hmm, odd, let me have a look ! and why is this blocking you?

Simply because I'm implementing tests in stub and a downstream process expects the existence of the `tbi` files!

Are you adding tests to oncoanalyser or something downstream of it ?

Something downstream! :slightly_smiling_face:

In fact, we're building a cascade pipeline that runs `oncoanalyser` itself and then downstream additions!

That is why the tests depend on the stub behaviour of `oncoanalyser`.
Hope that makes it more clear!

Definitely does ! Thanks for clarifying :slightly_smiling_face:

Curious to hear what you're building downstream as well

You're welcome! :slightly_smiling_face:

These are still WIP repositories, but there's already some information there:
• Cascade - <https://github.com/Clinical-Genomics/oncoflow|github.com/Clinical-Genomics/oncoflow>
• Downstream pipeline - <https://github.com/Clinical-Genomics/oncorefiner|github.com/Clinical-Genomics/oncorefiner>
`oncorefiner` is a simple add-on pipeline which adds some annotation to the output `vcf` files and runs some additional tools to produce results that are compatible with our visualisation platform and match what the clinicians are used to receiving!

Interesting work, and in regards to the PR, it won't pass the built-in ci tests until adjustments for strict syntax are applied and also probably until the new template is merged

There are a swath of changes imminent for the 3.0.0 release that will support strict syntax and co, and <@U09P9LAESTF> I'll make sure the PURPLE stubs generate expected tbi as part of these changes for the next release

I see you've created a couple other issues too, realistically we'll be able to look at the file content snapshots and invalid gzip files for the 3.0.0 release

Oh that's great! Thank you both!

Then in the meantime I can point to my own fork of `oncoanalyser` so we can move on with development. And then as soon as the new release is out, we can use that!

Let me know if you'd like me to do anything else regarding this PR though! :slightly_smiling_face: