variant_calling: Minimal and fast pipeline for calling short variants (germline only) from targetted amplicons sequenced using the illumina long amplicon protocol. can be used as a generalised quick and dirty variant caller for small sequencing projects.
- to do:
- build docker container for the software
- remove filepaths and generalise
- create config /parameter files
rna_seq: General purpoise RNA-Seq / RNA-exome pipeline configured for running in AWS SSO environment, work in progress, move to seprate repo when production ready
- to do:
- finish building contianers and pushing to ECR
- finalise nextflow script
- move processes to modules
- build basespace transfer container