v0.11.0

• Use minimap2 instead of BWA. This code will work on existing reference directories made by clockwork reference_prepare. It will use the FASTA file in the directory. But if you rerun clockwork reference_prepare then it will make a minimap2 index file, saving indexing on the fly. This probably makes little difference for variant calling, but could make a difference when running decontamination because that reference is huge.
• Auto build singularity and docker containers
• Updates to the decontamination reference download scripts because accessions change etc.