Small steps - First working version

qbic-pipelines / vcftomaf

MIT License

9 stars 5 forks source link

Small steps - First working version #1

Closed SusiJo closed 10 months ago

SusiJo commented 11 months ago

PR checklist

[ ] 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 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.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).

SusiJo commented 11 months ago

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 commented 11 months ago

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.

SusiJo commented 11 months ago

: 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 commented 11 months ago

: 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 commented 10 months ago

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