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V1.2.1. Release #69

Merged
merged 17 commits into from
Sep 11, 2024
Merged

V1.2.1. Release #69

merged 17 commits into from
Sep 11, 2024

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dthoward96
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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.

erikwolfsohn and others added 17 commits August 15, 2024 04:15
@erikwolfsohn
in the GISAID covCLI workflow: addressed issues w/metadata formatting…
d2a65d9 
… & output file parsing. Added some additional error handling to prevent submission failures.
@erikwolfsohn
Prevent failures when:
fe7f44f 
optional biosample/sra columns are empty
bs-description is not present
@erikwolfsohn
Added check for empty columns before attempting to drop them.
4cfc3a1
@erikwolfsohn
warn when submitting sra and biosample together while Link_Sample_Bet…
542e3d0 
…ween_NCBI_Databases is disabled
@erikwolfsohn
removed code preventing prod submissions, made sure bs-description on…
1a57c29 
…ly created when biosample is being submitted, fixed capitalization
@erikwolfsohn
add handling for GISAID submission when samples have previously been …
74e0cc4 
…registered in GISAID
@erikwolfsohn
make fasta optional - not required for biosample/sra submission.
d5efaa0
@erikwolfsohn
for column w/ mix of data & blank values, don't write empty values to…
de4a25f 
… biosample or SRA attributes. this is applicable when:

-biosample: submitting multiple pathogens under same biosample template w/different optional fields
-SRA: submitting mix of single & paired end reads
@erikwolfsohn
use titles for individual sra runs if they exist, otherwise apply gen…
24a0deb 
…eral submission title
@erikwolfsohn
change check for empty title columns
4bf0c27
@erikwolfsohn
Merge branch 'seqsender_gisaid_dev' of github.com:erikwolfsohn/seqsen…
aed3c3e 
…der into seqsender_gisaid_dev
@erikwolfsohn
remove unused json reference
a4fff17
@dthoward96
Merge pull request #64 from erikwolfsohn/seqsender_gisaid_dev
971bfba 
GISAID covCLI bugfixes & BioSample/SRA modifications
@dthoward96
v1.2.1 release
73ef85b
@dthoward96
Merge pull request #68 from CDCgov/master
66e211f 
Update issue templates (#66)
@dthoward96
v1.2.1 Release
c13937a
@dthoward96
Merge branch 'v1.2.1.-Bug-Fixes-Update' of https://github.com/CDCgov/…
fde148c 
…seqsender into v1.2.1.-Bug-Fixes-Update
@dthoward96 dthoward96 merged commit fcc0410 into master Sep 11, 2024
2 checks passed
@dthoward96 dthoward96 deleted the v1.2.1.-Bug-Fixes-Update branch September 11, 2024 14:18
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@dthoward96 @erikwolfsohn