V1.3.2

V1.3.2 Release of SeqSender

Changes:

SeqSender:

• SeqSender will force columns that are expected to be uppercase for "submission_log.csv" in order to prevent error where column could become lowercase and validator would error out.
  • Organism", "Database", "Submission_Type", "Submission_Status", "Submission_ID"

What's Changed

• v1.3.2 upload log bug fix by @dthoward96 in #110

Full Changelog: v1.3.1...v1.3.2

V1.3.1

V1.3.1 Release of SeqSender

Changes:

SeqSender:

• Fixes a bug where how the database submission options were selected would cause SeqSender to be unable to find the validation schema for the config file resulting in a error.
  • Example: When selecting databases via "-bsgn" would not cause an error but "-b -s -g -n", which is a valid submission option would cause the identifiers used to identify the correct file to swap resulting in SeqSender to be unable to find the correct file.

What's Changed

• Update test data by @dthoward96 in #108
• v1.3.1 Bug Fix by @dthoward96 in #109

Full Changelog: v1.3.0...v1.3.1

V1.3.0

V1.2.7 Release of SeqSender

Changes:

SeqSender metadata options updated per: https://www.chcoc.gov/content/initial-guidance-regarding-president-trump%E2%80%99s-executive-order-defending-women

BioSample:

• SeqSender field for "gender_restroom" has been removed from metadata templates/validation.

GISAID:

• SeqSender field "gs-gender" has been changed to "gs-sex".
• SeqSender field "gs-Host_Gender" has been changed to "gs-Host_Sex".
• Automation for validating metadata has been updated to these new field names.

What's Changed

• fix version number by @dthoward96 in #106
• v1.3.0 Update by @dthoward96 in #107

Full Changelog: v1.2.7...v1.3.0

V1.2.7 Release

V1.2.7 Release of SeqSender

Changes:

GISAID:

• Add's support for epiRSV and add's metadata template for epiRSV to submission wizard.

What's Changed

• V1.2.7 by @dthoward96 in #104

Full Changelog: v1.2.6...v1.2.7

V1.2.6 Release

V1.2.6 Release of SeqSender

Changes:

• NCBI:
  • GenBank:
    • As part of recent changes to GenBank, some fields are now required, have been renamed, or deprecated and can no longer be used for submission. Please be sure to update your submissions accordingly.
    • "src-Host" and "src-Isolate" are now required fields.
    • "src-Country" has been renamed to "src-geo_loc_name". As per changes required by the INSDC. The field now is capable of holding additional location information. Additional region or locality information must be after the country, ocean, or major sea name and separated by a ':'. For example: USA: Riverview Park, Ripkentown, MD. For all available country names: http://www.insdc.org/documents/country-qualifier-vocabulary.
    • Deprecated Columns: "src-Authority", "src-Biotype", "src-Biovar", "src-Chemovar", "src-Forma", "src-Forma_specialis", "src-Identified_by", "src-Pathovar", "src-Pop_variant", "src-Serogroup", "src-Subclone", "src-Subtype", "src-Substrain", "src-Type"
  • BioSample:
    • Resolves NCBI submission bug for BioSample xml not validating against schema, missing descriptor. Metadata field for biosample submissions bs-sample_title is now a required field to resolve this issue.

What's Changed

• V1.2.6 Update by @dthoward96 in #101
• v1.2.6 update by @dthoward96 in #102

Full Changelog: v1.2.5...v1.2.6

V1.2.5 Release

V1.2.5 Release of SeqSender

Changes:

• NCBI/GISAID:
  • Validation of config file username/password now allows more special characters.

What's Changed

• V1.2.5 Update by @dthoward96 in #99

Full Changelog: v1.2.4...v1.2.5

V1.2.4 Release

V1.2.4 Release of SeqSender

Changes:

GenBank:

• Fixes bug where if submitting only to GenBank/GenBank is final database processing, "submission_status" command does not see flag correctly for processing submission and ignores updating status.

What's Changed

• V1.2.4 Update by @dthoward96 in #93

Full Changelog: v1.2.3...v1.2.4

v1.2.3 Release

v1.2.3 Release of SeqSender

Changes:

BioSample/SRA:

• Fixes bug where if submitting only one sample to BioSample/SRA, file "submission_status_report.csv" is not correctly updated with accession for sample because "report.xml" is not processed correctly.
• Added error handling for when "submission_status_report.csv" has no accessions to be updated but submission status is marked as "Processed".

What's Changed

• GitHub action test by @dthoward96 in #83
• V1.2.3 Update by @dthoward96 in #85

Full Changelog: v1.2.2...v1.2.3

V1.2.2 Release

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

• Merge pull request #72 from CDCgov/dev by @dthoward96 in #76
• v1.2.1 documentation typos fixes by @dthoward96 in #77
• Update issue templates by @dthoward96 in #79
• update dev by @dthoward96 in #81
• V1.2.2 Update by @dthoward96 in #82

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

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

• Update README.md (#61) by @dthoward96 in #62
• Update README.md by @dthoward96 in #63
• Update issue templates by @dthoward96 in #66
• GISAID covCLI bugfixes & BioSample/SRA modifications by @erikwolfsohn in #64
• Update issue templates (#66) by @dthoward96 in #68
• V1.2.1. Release by @dthoward96 in #69
• Dthoward96 remove cli by @dthoward96 in #70
• Update dev to v1.2.1 by @dthoward96 in #71
• Dev Update Readme by @dthoward96 in #72

New Contributors

• @erikwolfsohn made their first contribution in #64

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