Add bug fixes from master to v1.2.0 #52
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remove unwanted files
Final merged
* Delete .github/workflows/codeql-analysis.yml * Delete .github/workflows/python-package-mamba.yml
Missing a return for config file function and correcting a error message to print the correct df
* Create GHCR_docker.yml * Update GHCR_docker.yml Correct changes for master branch
Some FTP accounts have the folder structure /submit/Production/ instead of /Production/. This fix automatically corrects for this difference in folder structure.
update template metadata with required fields for flu
removed the gs-sequence_name specified for flu
Update process.py
automatic test builds dockerfile on pull request. This will prevent merging to master if Dockerfile fails to build correctly.
* Update cov_config.yaml remove org_id from examples * Update flu_config.yaml remove org_id from examples * Update create.py remove org_id from xml creation
* Update report.py Bug fix to allow for other submit folders in FTP of ncbi * Update process.py bug fix for capitalization of folder name
Changes requirement from only isolate to require either strain or isolate for BioSample and GenBank
Fixes issue that creates duplicate strain columns when using src-strain
Bug fix for upload log. When only one database was submitted it, it would convert the database name into a list and error out.
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had to rebuild cache after branch naming issue |
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