Deleted cwl/conda/picrust2_env.yml, cwl/docker-compose/irods/Dockerfile, cwl/docker-compose/rancher/Dockerfile, cwl/docker-compose/docker-compose.yml, cwl/files/user-settings.mkfg, cwl/irods/.gitkeep, cwl/irods/irods_environment.json, cwl/kube_instance/deploy.sh, cwl/kube_instance/nodes.txt, cwl/kube_instance/template_instance.yaml, cwl/scripts/Renviron, cwl/scripts/clustalo.py, cwl/scripts/connect.py, cwl/scripts/deploy.sh, cwl/scripts/install2.R, cwl/scripts/jobManager.sh, cwl/scripts/jobManagerENA.sh, cwl/scripts/metadata.py, cwl/scripts/reads.py, cwl/scripts/setup_workflow.sh, cwl/scripts/upload.sh, cwl/scripts/upload2.sh, cwl/Dockerfile, cwl/build.sh, cwl/build_test.sh, cwl/execute.sh, cwl/gitconfig, cwl/gitlab-admin-service-account.yaml, cwl/run.sh, irods/Dockerfile, irods/build.sh, notebook/graphdb/Dockerfile, notebook/jupyter/Dockerfile, notebook/jupyter/requirements.txt, notebook/rstudio/Dockerfile, notebook/build.sh, notebook/docker-compose.yml, .gitignore