- Add RNAseq sanity/QC checks https://github.com/genome/analysis-workflows/issues/904
- Add input type fastqs to RNA seq https://github.com/genome/analysis-workflows/issues/932
- bam-readcount release
- convert all pipelines to use cram throughout https://github.com/genome/analysis-workflows/issues/942
- Upgrade to BWA-MEM2 https://github.com/genome/analysis-workflows/issues/913
- Scatter Varscan calling in somatic WGS workflow - Tom Mooney https://github.com/genome/analysis-workflows/issues/921
- MarkDuplicates Spark implementation https://github.com/genome/analysis-workflows/issues/922
- Work on a Joint genotype workflow https://github.com/genome/analysis-workflows/issues/929
- Add DoCM documentation: https://github.com/genome/analysis-workflows/issues/833
- Remove Mills input https://github.com/genome/analysis-workflows/issues/868
- Review software for upgrades (pick one or two!) https://github.com/genome/analysis-workflows/issues/948
- Clean up bam indexing (and VCF?) https://github.com/genome/analysis-workflows/issues/738
- Make sure all alignment workflows accept sequence (bam/fastq) inputs https://github.com/genome/analysis-workflows/issues/935
- germline wgs workflow