Dependencies¶

Nextflow [Required]¶

• Nextflow

Singularity OR Docker [sarscov2 ONLY]¶

Either can be deployed within the nextflow.config file by setting the profile as singularity or docker during runtime - Singularity or Docker

Basespace [sarscov2 ONLY]¶

To access the sequencing files, the basespace cli must be installed. -Basespace

GISAID [gisaid ONLY]¶

To upload to GISAID, the gisaid cli must be installed. Prior to use the GISAID CLI requires authentication. Authentication must be performed every 100 days.

# Example test authentication
cli2 authenticate --client_id TEST-EA76875B00C3 --username sevillas2

# Example full authentication
cli2 authenticate --cliend_id [insert id] --username [username]

Python¶

Python3 is required to run quality control report scripts.

R¶

R version 4.3 is require to run analytical report scripts.