Picking up on a discussion I've had with @Maxime Garcia in the distant past: I've tried to implement some additional validation checks into my own pipeline to deal with gatk read groups. It's not only checking for lanes though, but also for flowcells and libraries (i.e. a biological sample is allowed to have multiple fastq (pair) entries in the samplesheet, as long as they differ in lane or flowcell, and those that differ in flowcell can share a lane). Samples labelled as coming from the same biological sample, but different libraries, are also treated correctly now by downstream GATK tools. Checks happen during samplesheet parsing, but also modify metamap to contain a

sample_LIB_LANE_FC

id. There's also some functions that tries to extract this info from either the file name or the fastq headers (based on sarek's current implementation actually 😉 ). If sarek currently also has this functionality too, just ignore this, but if it sounds interesting, feel free to reach out. (WIP code: https://github.com/ITMmalaria/plasmovar/blob/dev/subworkflows/local/utils_nfcore_plasmovar_pipeline/main.nf)

Oh yeah, I remember that convo

plz don't trigger my imposter syndrome thank you very much

Let's go over in #C05V9FRJYMV

(

#sarek-dev

from the nf-core slack)