This is a simple pipeline for taking in a list of CRAM files, converting them to BAM files, and then using telseq for telomere length estimation. The pipeline uses cromwell as the workflow tool. The computational backend is intended to be google compute, which uses the google pipelines / job-execution-as-service API to launch jobs in docker containers. Docker containers for this pipeline can be found here docker hub. This pipeline is under heavy development and is not recommended for production use. Alternative methods for telomere length estimation will be added in the future.
The hall-lab sv-pipeline was a valuable reference to consult.