Add UMI reads processing capability

[lescai]

nf-core/sarek pull request

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PR checklist

• This pull request introduces a chunk of code to process reads containing UMIs. Unique Molecular Indices are very important particularly for somatic workflows aiming at detecting very low allele-fraction variants (MRD, Liquid Biopsy). The chosen workflow adopts the FGBIO tools, which create a consensus read within the same UMI-groups, and a robust method for identification of the groups. See blog and ref.
  The approach ensures downstream compatibility with the workflow: the result of the UMI process is a uBam, which can then be fed into MappingReads and downstream in both HaplotypeCaller and more importantly Mutect2 or Strelka.

• Tests are work in progress: datasets have been identified from 2 different UMI types (QIAseq and Illumina TSO), but cannot complete them on laptop

• As indicated above, the reads will be uploaded at nf-core/sarek branch on the nf-core/test-datasets repo

• The code has passed lints (nf-core lint .).

• Documentation in docs has been updated

• CHANGELOG.md is not been updated yet

• README.md has not been updated yet (not sure if this is relevant)

[maxulysse]

Looks amazing.
We just need the test data to do some CI.
Can you update the CHANGELOG as well?

[maxulysse]

Made a couple of suggestions, if you accept them, you can batch commit them.

[lescai]

agree with suggestions, reviewed and made more explicit

[chelauk]

Hi any updates on adding umi to variant calling? Is it working? Otherwise I will build a new pipeline.

[lescai]

Hi @chelauk not sure what's holding the pull request at this stage, I did test everything at the March hackathon using the test data here
https://github.com/nibscles/test-datasets/tree/sarek-umi
And it's working.
We are using our standalone code at NIBSC, if you don't want to build something new: it's undocumented, but it will give you an unmapped BAM, which you can then feed into Sarek if you like.
https://github.com/nibscbioinformatics/core/tree/master/workflows/umi
The important thing is to pass the correct UMI structure (see documentation for this pull request)
https://github.com/nibscles/sarek/blob/umi/docs/usage.md#--umi

[maxulysse]

Hi @chelauk @nibscles
I wanted to close this one during the hackathon, but did not find the time.
I'll make sure merge it by the end of the week.
We're planning a minor release soonish as well

[maxulysse]

@chelauk @nibscles
PR is finally merged.
I'll be making another PR regarding UMI, some tiny code polishing and adding test.