A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi, I have a question about paired sample mode. I will have some data where I have one FASTQ from a wild type sample and several FASTQs from different mutant lines (separate specimen, not timepoints). Will the pipeline behave correctly if I enter the WT as "normal" and each mutant as "tumour" with the same "patient" ID, or do I need a more elaborate approach?

for me normal =~ WT, and tumor =~ mutants

Will it work fine if I have multiple mutants? e.g.
```patient,sample,status,...
gene1,wildtype,0,...
gene1,mutant1,1,...
gene1,mutant2,1,...```

yeah, sarek can handle multiple different tumors belonging to the same patient

As you might want to compare normal to different tumors, and figure out how they diverged

It worked and it's amazing, variant count reduced by almost 3 orders of magnitude