Pangolin_Update

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Genomic Characterization	Viral, SARS-Cov-2	PHB v2.0.0	Yes	Sample-level

Pangolin_Update_PHB

The Pangolin_Update workflow re-runs Pangolin updating prior lineage calls from one docker image to meet the lineage calls specified in an alternative docker image. The most common use case for this is updating lineage calls to be up-to-date with the latest Pangolin nomenclature by using the latest available Pangolin docker image (found here).

Inputs

This workflow runs on the sample level.

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
pangolin_update	assembly_fasta	File	SARS-CoV-2 assembly file in FASTA format		Required
pangolin_update	old_lineage	String	The Pangolin lineage previously assigned to the sample		Required
pangolin_update	old_pangolin_assignment_version	String	Version of the Pangolin software previously used for lineage assignment.		Required
pangolin_update	old_pangolin_docker	String	The Pangolin docker image previously used for lineage assignment.		Required
pangolin_update	old_pangolin_versions	String	All pangolin software and database versions previously used for lineage assignment.		Required
pangolin_update	samplename	String	The name of the sample being analyzed.		Required
pangolin_update	lineage_log	File	TSV file detailing previous lineage assignments and software versions for this sample.		Optional
pangolin_update	new_pangolin_docker	String	The Pangolin docker image used to update the Pangolin lineage assignments.		Optional
pangolin4	analysis_mode	String	Pangolin inference engine for lineage designations (usher or pangolearn)	None	Optional
pangolin4	cpu	Int	Number of CPUs to allocate to the task	4	Optional
pangolin4	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
pangolin4	expanded_lineage	Boolean	True/False that determines if a lineage should be expanded without aliases (e.g., BA.1 → B.1.1.529.1)	TRUE	Optional
pangolin4	max_ambig	Float	Maximum proportion of Ns allowed for Pangolin to attempt assignment	0.5	Optional
pangolin4	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional
pangolin4	min_length	Int	Minimum query length allowed for pangolin to attempt assignment	10000	Optional
pangolin4	pangolin_arguments	String	Optional arguments for pangolin e.g. "--skip-scorpio"	None	Optional
pangolin4	skip_designation_cache	Boolean	True/False that determines if the designation cache should be used	FALSE	Optional
pangolin4	skip_scorpio	Boolean	True/False that determines if scorpio should be skipped.	FALSE	Optional
pangolin_update_log	cpu	Int	Number of CPUs to allocate to the task	4	Optional
pangolin_update_log	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
pangolin_update_log	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/utility:1.1	Optional
pangolin_update_log	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional
pangolin_update_log	timezone	String			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
pango_lineage	String	Pango lineage as determined by Pangolin
pango_lineage_expanded	String	Pango lineage without use of aliases; e.g., BA.1 → B.1.1.529.1
pango_lineage_log	File	TSV file listing Pangolin lineage assignments and software versions for this sample
pango_lineage_report	File	Full Pango lineage report generated by Pangolin
pangolin_assignment_version	String	Version of the Pangolin software (e.g. PANGO or PUSHER) used for lineage assignment
pangolin_conflict	String	Number of lineage conflicts as determined by Pangolin
pangolin_docker	String	The Docker container to use for the task
pangolin_notes	String	Lineage notes as determined by Pangolin
pangolin_update_analysis_date	String	Date of analysis
pangolin_update_version	String	Version of the Public Health Bioinformatics (PHB) repository used
pangolin_updates	String	Result of Pangolin Update (lineage changed versus unchanged) with lineage assignment and date of analysis
pangolin_versions	String	All Pangolin software and database versions