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nf-core / demultiplex

Demultiplexing pipeline for sequencing data
https://nf-co.re/demultiplex
MIT License
41 stars 36 forks source link

UMI handling for DEMUX pipeline #200

Closed apeltzer closed 1 month ago

apeltzer commented 1 month ago

Add UMI handling feature to demux pipeline that extracts the UMIs from input files and then adds the UMI to the respective fastq header.

grst commented 1 month ago

Does it make sense to have this in the demux workflow? Personally I'd rather keep manipulations to the fastq files minimal and leave it to downstream workflows to deal with UMIs and the like.

apeltzer commented 1 month ago

Fair enough, that issue was only raised via me but I tend to have the same opinion on this one too 👍🏻 Lets not do it and instead rather get downstream workflows to tackle this appropriately (rnaseq, sarek, smrnaseq can all do it).