Small steps - First working version

[SusiJo]

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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/vcftomaf branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[SusiJo]

Comment: The pipeline was also tested with sarek vcf files from different variant callers (from aws-megatests) and was working fine. When specifying a samplesheet it is important to give unique sample names in the first column though.

[mirpedrol]

When specifying a samplesheet it is important to give unique sample names in the first column though

You can use the unique key in the samplesheet.

[FriederikeHanssen]

Great work, Susi! Very useful to have this in a proper pipeline finally. there is some branding left that should probably be removed. I have marked it where I found it.

Another thought I had: we will in 99% of cases use this pipeline with sarek. i would vote for having the same igenomes config here as we do in sarek to make it as straightforward as possible to choose the right reference

[SusiJo]

: we will in 99% of cases use this pipeline with sarek. i would vote for having the same igenomes config here as we do in sarek to make it as straightforward as possible to choose the right reference

Should I remove the unnecessary lines or use the sarek igenomes.config as is?

[FriederikeHanssen]

: we will in 99% of cases use this pipeline with sarek. i would vote for having the same igenomes config here as we do in sarek to make it as straightforward as possible to choose the right reference

Should I remove the unnecessary lines or use the sarek igenomes.config as is?

I would prob just use the sarek conf (at least that is what i did in the createpanel pipeline) less work and ensures the keys really are the same

[FriederikeHanssen]

Can we merge this @skrakau ? I'd like to test it out and add what is missing. would be easier on my fork...

[FriederikeHanssen]

merging to test