Release 4.0.0

Changes from Previous Release (v3.1.0):

(1) New, streamlined submission code

• Supports ftp submission to GenBank (SARS-CoV-2, influenza, and bacteria)
• GenBank ftp submission uses table2asn (v1.28.1179) to prepare an ASN.1 file, authorset.sbt file, and comment.cmt file and uploads these to NCBI along with a submission.xml file.
• Still support non-ftp GenBank submission, either manually (send the email yourself) or automatically send submission to user and NCBI GenBank submission team. This mode uses table2asn to prepare an ASN.1 file, authorset.sbt, comment.cmt, and source.src file. IT also creates a zip file of these extra table2asn outputs.
• Change name of raw fastq files to <sample_name>_R{1,2}.fastq.gz (important: code assumes your fastq files are gzipped) before ftp upload to SRA repository.
• Added support for SRA publication hold (delayed release)
• Note: Submissions are currently completed one sample at a time. Batch submissions coming soon.
• SFTP support added (still in beta testing)

(2) Minor corrections to metadata files

• Two columns adjusted to clarify input and to match NCBI attribute name (age and sex --> host_age and host_sex)
• Extraneous "description" column removed from metadata files
• gff_path added to some test metadata files where it was missing
• "Cdiphtheriae" changed to "bacteria" in test data, for added clarity

(4) Environment changes and upgrades

• table2asn added to environment.yml file
• nameparser (v1.0.5) python library added to environment.yml file
• paramiko (v3.4.0) python library added to environment.yml file

(3) Bug fixes

• Several bug fixes were made along the way...

βeta3

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:

• Template for Git Issues by @ankushkgupta2 in #12
• New Issue Templates + Default Labels and Titles - Issue #18 by @ankushkgupta2 in #19
• README.md Improvements (Issue #26) by @ankushkgupta2 in #30
• Residual README.md Changes From PR #30 (Root: Issue #26) by @ankushkgupta2 in #31
• VADR Annotation Integration by @ankushkgupta2 in #28
• Updates to Issue / PR Temps by @ankushkgupta2 in #24
• Maintainer Contact + Issue Request Information by @ankushkgupta2 in #23
• Patch for VADR Enhancement and Parameter Check Changes by @ankushkgupta2 in #32

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

βeta2

Added Functionality:

(1) Ability to easily specify a database for sample submission through the Nextflow wrapper (submission_database)

(2) Pre-existing email functionality, for notifying user during a Genbank submission with genbank_submission_type set to table2asn, is now configurable within the Nextflow wrapper

• Functionality is toggled on/off with send_submission_email
• Email recipient is specified as a new field within your submission config under 'general' as 'notif_email_recipient'

(3) Git submodule integration of internal CDC submission configs with the repository

• Configs exist in a remote GitLab repository with permissions limited to CDC personnel with access to the Monkeypox group
• Documentation outlining steps on how to initialize the submodule and pull these config files from the remote location to your local version of the repo is specified within docs/cdc_configs_access.md

(4) Fully Nextflow Tower compatible

• Docker container is now hosted DockerHub and can automatically be pulled in (assuming you have the proper permissions)
• Rewriting/refactoring of the Python scripts handling database submission via FTP
• Enhancements of Nextflow wrapper structure/code to now scale across various environments

(5) Updates to README.md to include these latest changes (new/removed parameters, general restructuring etc.), as well as updates to PULL_REQUEST_TEMPLATE.md

βeta

First release for Beta Testing.