Terra_2_GISAID

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Public Data Sharing	Viral	PHB v1.2.1	Yes	Set-level

Terra_2_GISAID_PHB

Terra_2_GISAID programmatically submits SARS-CoV-2 assembly files to GISAID.

This workflow expects data that has been prepared for submission using either Mercury_Batch or Mercury_Prep_N_Batch (recommended).

client-ID

To obtain a client-ID, contact clisupport@gisaid.org and include your username in your request.

Inputs

The optional variable frameshift_notification has three options that correspond to the associated web-browser options:

• "catch_all" - "Notify me about ALL DETECTED FRAMESHIFTS in this submission for reconfirmation of affected sequences"
• "catch_novel" [DEFAULT] - "Notify me only about NOT PREVIOUSLY REPORTED FRAMESHIFTS in this submission for reconfirmation of affected sequences"
• "catch_none" - "I confirm ANY FRAMESHIFTS in this submission and request their release without confirmation by a curator"

GISAID Credentials

Please note that the user must provide either an authentication_file or a gisaid_credentials file to run this workflow; explanations for both can be found in the table below.

This workflow runs on the sample level.

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
Terra_2_GISAID	client_id	String	This value should be filled with the client-ID provided by GISAID		Required
Terra_2_GISAID	concatenated_fastas	File	The GISAID FASTA file generated by Mercury_Prep_N_Batch (or Mercury_Prep)		Required
Terra_2_GISAID	concatenated_metadata	File	The GISAID metadata file generated by Mercury_Prep_N_Batch (or Mercury_Prep)		Required
gisaid_upload	authentication_file	File	[EITHER] The GISAID authentication file generated by running cli3 authenticate for the submitter.		Optional, Required
gisaid_upload	cpu	Int	Number of CPUs to allocate to the task	1	Optional
gisaid_upload	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
gisaid_upload	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/broadinstitute/gisaid-cli:3.0	Optional
gisaid_upload	frameshift_notification	String	See top of inputs section for explanation; the notification preference regarding frameshifts in your submission	catch_novel	Optional
gisaid_upload	gisaid_credentials	File	[EITHER] A tab-delimited file containing the submitter's GISAID username followed by their password, used to generate the GISAID authentication file.		Optional, Required
gisaid_upload	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	2	Optional
version_capture	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0"	Optional
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional

Outputs

Variable	Type	Description
failed_uploads	Boolean	The metadata for any failed uploads
gisaid_cli_version	String	The verison of the GISAID CLI tool
gisaid_logs	File	The log files regarding the submission
terra_2_gisaid_analysis_date	String	The date of the analysis
terra_2_gisaid_version	String	The version of the PHB repository that this workflow is hosted in