V1.2.0 Release

V1.2.0 Update of SeqSender:

Note: When upgrading to V1.2.0, some files have changed. Before upgrading your current version, finish processing any of your current submissions before completing the update. To see the new changes, use the "Submission Wizard" in the updated documentation to generate a new config file and to view the updated metadata fields required for submitting samples with SeqSender.

Updates:

• SeqSender now supports more submission options.
  • All GISAID epiCLI database tools are now supported. EpiFLU, EpiCoV, EpiArbo, EpiRSV, EpiPox
  • All BioSample Packages are now supported.
  • All organisms can now be submitted to NCBI via SRA, BioSample, and GenBank via table2asn.
• Now generates all supported databases, manual submission files for when submitting via GUI web portals.
• NCBI database submissions can now be made with holdback dates, allowing users to upload their data to NCBI and choose when it is released to the public.
• Metadata is now validated for submission errors before performing submission, including when generating files for manual submission.
• Documentation has been overhauled to include detailed descriptions of all functions and interactivity. Users can now create and generate the correct config file and metadata fields needed for submitting samples via SeqSender.
• Logging and output files from SeqSender are now standardized with detailed explanations of output fields in updated documentation.

What's Changed

• Final merged v1.1.0 by @dthoward96 in #18
• Delete .github/workflows/codeql-analysis.yml by @dthoward96 in #19
• Update README.md by @dthoward96 in #21
• Create pkg_down.yaml by @dthoward96 in #20
• Rename pkg_down.yaml to pkgdown.yaml by @dthoward96 in #22
• Create codeql-analysis.yml by @dthoward96 in #24
• Create python-package-mamba.yml by @dthoward96 in #26
• Final merged by @dthoward96 in #23
• remove unwanted files by @rchau88 in #27
• Final merged by @rchau88 in #28
• Create codeql-analysis.yml by @dthoward96 in #25
• Create codeql.yml by @dthoward96 in #29
• Dthoward96 workflow correction by @dthoward96 in #30
• Add files via upload by @dthoward96 in #31
• bug fix process.py by @dthoward96 in #32
• Create GHCR_docker.yml by @dthoward96 in #33
• FTP folder bug fix submit.py by @dthoward96 in #34
• update template metadata with required fields for flu by @rchau88 in #37
• Update process.py by @rchau88 in #39
• Create docker_test_build.yml by @dthoward96 in #41
• Dthoward96 org id patch by @dthoward96 in #42
• Dthoward96 bugfix by @dthoward96 in #45
• add either or for strain/isolate by @dthoward96 in #49
• create.py duplicate strain name bug by @dthoward96 in #50
• Bug fix process.py by @dthoward96 in #51
• Bug fix for gisaid name overwriting genbank name for fasta file by @dthoward96 in #53
• bug fix fasta file creation by @dthoward96 in #55
• Bug fix create.py by @dthoward96 in #56
• Table2asn bug fixes by @dthoward96 in #57
• V1.2.0 Update by @dthoward96 in #58
• V1.2.0 Prod Update by @dthoward96 in #60
• Update README.md by @dthoward96 in #61

Full Changelog: https://github.com/CDCgov/seqsender/commits/v1.2.0