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docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

dockerfiles

gisaid-cli

Docker container with GISAID-provided CLI tools

lyve-set

:dancer: :palm_tree: LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

nextstrain_salmonella

backup for nextstrain salmonella workflow

parallel-fastq-dump

parallel fastq-dump wrapper

public_health_bacterial_genomics

public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

terra_api_wrappers

Scripts to wrap Terra API calls for programmatic workflow execution, workspace management, and data export to other platforms. Part of the workflow is specific to my environment, but hopefully it all can be useful for anyone working in Terra.

terra_utilities

usher-public-workflow

A Dockstore WDL Workflow that uses UShER to place your consensus.fasta sequences on the SARS-CoV-2 phylogeny

wdl

Workflow Description Language - Specification and Implementations

wdl_pathogen_build

wdl_workflows