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Releases: CDCgov/seqsender

V1.2.2 Release

19 Sep 18:50
@dthoward96 dthoward96
v1.2.2
a08c840
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V1.2.2 Release Latest
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V1.2.2 Release of SeqSender

Changes:

GISAID:

  • FLU GISAID submission metadata now correctly parses partial collection dates. If only year is present, it is now correctly stored in "Collection_Year" and if/when month is also present, it is stored in "Collection_Month". If the entire "YYYY-MM-DD" collection date is present, it is stored in the "Collection_Date" field and "Collection_Year"/"Collection_Month" are left empty, otherwise, if the entire collection date is not present, "Collection_Date" is left empty. All fields are added regardless of whether there are only partial/complete dates present.
  • FLU template/validation metadata has additional fields added.
    • Sampling_Strategy
    • Sequencing_Strategy
    • Sequencing_Technology
    • Assembly_Method
    • Coverage
    • Adamantanes_Resistance_pheno
    • Oseltamivir_Resistance_pheno
    • Zanamivir_Resistance_pheno
    • Peramivir_Resistance_pheno
    • Other_Resistance_pheno

What's Changed

Full Changelog: v1.2.1...v1.2.2

Contributors

dthoward96
Assets 2
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V1.2.1 Release

11 Sep 14:36
@dthoward96 dthoward96
v1.2.1
c2f308a
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V1.2.1 Release

V1.2.1 Release of SeqSender

Changes:

NOTE: Submission configs for NCBI databases have changed and some fields have been moved to the metadata file.
Config File:
Description: Title and Description: Comment have been removed from the config file and have been moved to the metadata as the fields "-title" and "-comment".
BioSample metadata changes:
Field "bs-description" has been replaced with the optional fields "bs-sample_title" and "bs-sample_description". This change eases submitting to BioSample as the "bs-description" field is not a attribute for biosample and is a descriptor field when uploading to BioSample. The Change of the fields allows for the user to have greater control over the input of these fields.
Shiny documentation changes:
Submission wizard bugs causing some fields to contain incorrect values for SeqSender have been resolved. Bugs with interactability of the submission wizard when selecting databases and editing the user config have been resolved.
GISAID submissions:
GISAID submission codebase has been overhauled to eliminate possible bugs related to submission differences between databases. With bugs related to generating GISAID submission files, interacting with epiCLI's, logging accessions being resolved.
Other:
Misc. bug fixes for other databases.

Full Changelog: v1.2.0...v1.2.1

What's Changed

New Contributors

Full Changelog: v1.2.0...v1.2.1

Contributors

erikwolfsohn and dthoward96
Assets 2
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V1.2.0 Release

06 Aug 20:36
@dthoward96 dthoward96
v1.2.0
61a756b
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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

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

Contributors

dthoward96 and rchau88
Assets 2
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