Related Issues (20)
- Add serotypefinder results to prp
- Cdm output format needs clarification and calculation fixes
- Add clarity lims id to output for bonsai input
- Serotypefinder empty results causes prp error
- Add pytests for annotate delly
- TypeError re coverage_uniformity
- Make insert size not required and fix is_paired()
- Add ShigaPass output to prp
- Add --input_dir to run create-bonsai-input on all jasen files in dir
- Pysam error when trying to read the bam file HOT 1
- Add species prediction from multiple softwares to PRP output
- Different datamodels are used when data is being read again
- Add drtype from tbprofiler output to bonsai input file
- Convert sample_id to be a combination of lims_id and seqrun
- Update parsing of TbProfiler results to support version 6
- Move sample name and lims id from RunInformation to Sample data model HOT 1
- Split RunInformation into sequencing and pipeline specific data.
- Split tbprofiler output into SNV and SV
- Update cgmlst model and parser regarding chewbbaca errors
- n_read_pairs needs to be divided by two
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