v8.0.0

What's Changed

• Updating github actions workflow by @RamiyapriyaS in #344
• Ick4 update submission by @jessicarowell in #345

NCBI allows UI-less updating of BioSample submissions, and TOSTADAS v8.0.0 can do this using the --workflow update_submission workflow option.

To submit updated metadata to biosample, use the following command:

nextflow run main.nf -profile <docker|singularity> --workflow update_submission --dry_run false --species mpxv --submission_config <path/to/submission_config.yaml> --original_submission_dir <results/mpxv_test_metadata/submission_outputs> --meta_path <path/to/updated/metadata/file>

Please make sure your updated metadata Excel file has a biosample_accession column that contains accurate accession IDs. TOSTADAS does not check these for accuracy. Please make sure they are correct.

Note: TOSTADAS uses the ncbi-spuid field to match samples in the metadata file and the original submission.xml. The sample_name field is not preserved in the submission.xml, so it cannot be used as an identifier for this workflow.

Full Changelog: v7.1.0...v8.0.0