CDCgov / CDCgov/seqsender

[FEATURE REQUEST] test submissions to all three databases

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enhancement
Dominant language
Python
Stars
2
Forks
0
Avg merge
20m
Merged PRs (30d)
5

Description

Is this feature for general SeqSender usage or for submitting to a specific database, if so what database?
I am trying to test the pipeline for all three databases (with flu) but there are three separate metadata files for each biosample, sra, and genbank.

Is your feature request related to a problem? If so please describe.
I have successfully run a test for genbank only but hoping to confirm all three databases can be successfully submitted to in one run. Please let me know if I am missing something!

this command successfully generated files for Genbank but didn't actually submit
docker run --rm -v $PWD/test_data/FLU/:/data seqsender bash /seqsender/seqsender-kickoff submit --genbank --organism FLU --submission_name 0807test --submission_dir /data --config_file /data/flu_ config.yaml --metadata_file /data/flu_genbank_metadata.csv --fasta_file /data/flu_sequence.fasta

I then ran this and it submitted via FTP

docker run --rm -v "$PWD/test_data/FLU:/data" seqsender bash /seqsender/seqsender-kickoff submission_status --submission_name 0807test --submission_dir /data

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the seqsender-kickoff submit command and the test_data/FLU files, including the three metadata files, flu_config.yaml, and flu_sequence.fasta. Determine how the existing GenBank-only run handles submission, then define and verify a single run that processes Biosample, SRA, and GenBank and reports their submission status.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
cli, data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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