Skip to content

βeta3

Pre-release
Pre-release

Choose a tag to compare

View all tags
@ankushkgupta2 ankushkgupta2 released this 13 Apr 15:41
v2.0.0-beta
22deebe
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

Changes from Previous Release (βeta2):

(1) New gene annotation pipeline (VADR) integrated into Nextflow wrapper:

  • Can be accessed through both the main workflow (using the run_vadr parameter) and as a separate entrypoint
  • VADR is restricted to only running through Docker, as the docker container is being pulled from the StaphB DockerHub (VADR Container). The actual docker container is specified via a new parameter: docker_container_vadr
  • If both Liftoff and VADR gene annotation are toggled on, for the main workflow, they will run in parallel during their respective processes and through the submission portion of the pipeline. VADR will output files in the directory defined by the vadr_output_dir parameter
  • Necessary MPXV model files for reference have been added to the repository, therefore no additional setup is required. A new parameter named vadr_models_dir has been added to encode the location of these model files

(2) New templates for opening an issue have been added:

  • bug related and opened by a maintainer/collaborator
  • feature related and opened by a maintainer/collaborator
  • bug related and opened by a user
  • feature related and opened by a user

The various options can be found here: Issues Tab

(3) Updates to the pull-request template:

  • custom checklist
  • CDC specific criteria (for maintainers/collaborators)

(4) README.md has had multiple changes including:

  • all information about VADR including where to find accompanying documentation for this package and the parameters mentioned above
  • general ordering with certain sections have been switched or change
  • information added in the setup section to include steps for provisioning a Scicomp (HPC Cluster at the CDC) environment to run the pipeline
  • certain pieces of information have been made present or more obvious within the quick-start and running the pipeline sections (wait time, setting up your submission configuration file, etc.)
  • more information has been added to explain required parameters/inputs for the submission entrypoints

(5) Test files (.yaml and .json) have been created within the nf_params directory

Autogenerated Release Notes:

Full Changelog: v1.0.0-beta...v2.0.0-beta

Contributors

ankushkgupta2
Assets 2
Loading