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SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
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RunVCFTools and RunBcftoolsStats are run twice for the same input #802

Closed alneberg closed 4 years ago

alneberg commented 5 years ago

Describe the bug RunVCFTools and RunBcftoolsStats are run both within germlineVC and annotation. From what I understand this is on the same input. Additionally, RunVCFTools is extremely slow for the gvcf file (almost 4 hours). See attached image of the timeline for germlineVC using tools Manta, Strelka and HaplotypeCaller.

Screen Shot 2019-05-16 at 11 16 42

I don't know if the best solution is to save this for annotation only perhaps? The benefit of having it in annotation is that it can be ran in parallel with the annotation processes instead of hogging up the analysis as it is currently.

Sarek (please complete the following information):

maxulysse commented 5 years ago

OK, so I'll disable VCF tools for g.vcf Do you want that for 2.3.FIX2, 2.4 or 2.5 ?

maxulysse commented 4 years ago

Done on nf-core/sarek