Add tumour-only mode - Githubissues

nf-core / rnadnavar

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

https://nf-co.re/rnadnavar

MIT License

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Add tumour-only mode #37

Open RaqManzano opened 3 months ago

RaqManzano commented 3 months ago

Description of feature

Generate tumour-only mode for variant calling. This should only affect to the variant_calling module of the pipeline, once we obtain the VCFs the rest of modules should behave the same.

TODOs:

[x] Review tumour-only subworkflows from sarek, starting from bam_variant_calling_tumor_only_all
[x] Add the appropriate subworkflows for the pipeline
[x] Create SAGE tumour only subworkflow
[ ] Testing
[ ] Check filtering in case some adjustments need to be done

RaqManzano commented 3 months ago

Have a working version of tumour only in a local branch, will push when testing is done.

f1lem0n commented 2 months ago

Hi! Any developments on this feature? I'd like to run some of my tumor-only samples through the pipeline :smile:

RaqManzano commented 1 month ago

A draft pull request is now live https://github.com/nf-core/rnadnavar/pull/43