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nf-core / fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
https://nf-co.re/fastquorum
MIT License
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Add additional metrics to MultiQC #46

Open nh13 opened 2 months ago

nh13 commented 2 months ago

Description of feature

See: https://github.com/nf-core/fastquorum/pull/42#discussion_r1608511337

E.g. add metrics produced by GroupReadsByUmi: See: https://github.com/MultiQC/MultiQC/blob/main/docs/modules/fgbio.md

Are there additional QC that we should add? It would be useful to have a table where each row is a sample, and each column is the # of reads after a given step. E.g. raw reads (mapped and grouped), consensus calls (total and mapped), filtered calls (total and mapped).

SPPearce commented 2 months ago

Oh yes, a summary of where the reads are "lost" would be really useful. Potentially also an on-target proportion as generally it is going to be used with a pulldown.