1.3.2 read group - can use only 1?

[RichardCorbett]

Is your feature request related to a problem? Please describe.
I have samples that are sequenced deeply and the data span multiple nanopore flowcells. When I merge those bams there will be multiple read group (I per flowcell). When I run medaka I get an error saying RuntimeError: The bam F24722_merged.bam contains more than one read group. Please specify --RG to select which read groupto process from {'272423_fastq_runid_9c2b42a90ae458fb58e19950f06b13da5ceede77', '272422_fastq_runid_5b33097e8a403b7ed7d030764f669d6be91d0ef4'}

How can I run medaka on all data in the bam without editing the read group information?

Describe the solution you'd like

Process multiple read groups if they have the same library and/or sample ID. Perhaps this is possible now, but I haven't found a way to do it.

[cjw85]

Apologies, this is not currently possibly. You will have to write a bam without read group information or with a single read group.

I cannot unfortunately give a timeline on implementing an --all_reads option.