CZGenEpi_Prep_PHB workflow

[sage-wright]

🛠️ Changes Being Made

This PR introduces the CZGenEpi_Prep workflow which prepares data for upload to the Chan Zuckerberg GEN EPI platform, where phylogenetic trees and additional data processing can occur.

🧠 Context and Rationale

Many Terra users are doing this process manually, and so we thought to give them a hand.

📋 Workflow/Task Steps

1. Download Terra table
2. Extract desired samples
3. Extract desired columns
4. Reformat fasta file header and concatenate fasta file
5. Celebrate 🎉

Inputs

Required

• sample_names : array of sample ids
• terra_project_name : name of project
• terra_table_name : name of table where data is
• terra_workspace_name : name of workspace

Optional
There are many optional variables so the user can specify whatever they want. I have listed the defaults below as well.

• assembly_fasta_column_name = "assembly_fasta"
• collection_date_column_name = "collection_date"
• private_id_column_name = terra_table_name + "_id"
• continent_column_name = "continent"
• country_column_name = "country"
• state_column_name = "state"
• county_column_name = "county"
• gisaid_id_column_name = "gisaid_accession"
• genbank_accession_column_name = "genbank_accession"
• sequencing_date_column_name = "sequencing_date"
• sample_is_private_column_name = "sample_is_private"

Outputs

• concatenated_czgenepi_fasta : the concatenated fasta file with the renamed headers (the headers are renamed to account for clearlabs data which has unique headers)
• concatenated_czgenepi_metadata : the concatenated metadata that was extracted from the terra table using the specified columns
• czgenepi_prep_version : the version of PHB the workflow is in
• czgenepi_prep_analysis_date : the date the workflow was run

🧪 Testing

Locally

Cannot test locally due to permissions.

Terra

Successful test here: https://app.terra.bio/#workspaces/cdc-terra-resources/Theiagen_Wright_SC2_Sandbox/job_history/f6ffd70e-ed78-48fe-8b59-f2178d228e63

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[jrotieno]

Works as expected!