bam_variant_calling_freebayes

[priyanka-surana]

A generic version of the freebayes subworkflow that can be imported to replace steps in sarek and mag

Modules included:

• SAMTOOLS_FAIDX
• FREEBAYES
• BCFTOOLS_SORT
• BCFTOOLS_INDEX

PR checklist

Closes #2215

• [ x] This comment contains a description of changes (with reason).
• [ x] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
• [ ] If necessary, include test data in your PR.
• [ x] Remove all TODO statements.
• [ x] Emit the versions.yml file.
• [ x] Follow the naming conventions.
• [ x] Follow the parameters requirements.
• [ x] Follow the input/output options guidelines.
• [ ] Add a resource label
• [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • [ ] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[matthdsm]

Could you also add a small readme describing the workflow steps in a diagram? https://mermaid-js.github.io/mermaid/#/ https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

[priyanka-surana]

Could you also add a small readme describing the workflow steps in a diagram? https://mermaid-js.github.io/mermaid/#/ https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

Where should I add this information?

[matthdsm]

A readme.md file next to main.nf seems allright 🤷🏻‍♂️ @Emiller88 , opinion?

[edmundmiller]

Yeah, I think a README.md in the dir should be the move. It should get rendered by GitHub then!

[priyanka-surana]

Yeah, I think a README.md in the dir should be the move. It should get rendered by GitHub then!

Should I wait till the tooling update is made or should I manually add it for this subworkflow?

[edmundmiller]

Should I wait till the tooling update is made or should I manually add it for this subworkflow?

Manually add it!

[priyanka-surana]

@Emiller88 @matthdsm I added a readme file with the mermaid flowchart. I am not at all familiar with mermaid so please make changes. Unless some of the meta.yml information is moving to readme.md, maybe call it a mermaid_flowchart.md or mermaid.md, much more clear.

[matthdsm]

Hi @priyanka-surana If you put the flowchart code inside a code block with the mermaid designator, it will automatically be rendered. so use

\```mermaid
\ flowchart TD
\ ...
\```

(ignore the backslashes)

[matthdsm]

Hi there!

We've noticed there hasn't been much activity here. Are you still planning on working on this? If not, you can ignore this message and we'll close your PR in about 2 weeks

Cheers the nf-core maintainers

[priyanka-surana]

The merging is blocked. I am not sure what additional changes are needed to merge this. I think that is why it got inactive.

[matthdsm]

Thanks for the reply @priyanka-surana, I've removed the stale review. Feel free to merge once the tests pass!

Matthias

[priyanka-surana]

I think the md5sums need updating. Will commit the changes later and merge.