orientation-files.md

Overview of this repository (i.e., what do these files do?)

The files in this repository fall into one of XXX categories:

• Input files
• Output files and directories
• Workflow configuration files we might want to customize
• Workflow configuration files we don't need to touch
• Documentation

We'll walk through these one by one; the 5 most important files are bolded.

Input files

Directory	File	Description	Configuration
./data/	sequences.fasta	Genomic sequences; IDs must match strain column in metadata.tsv	See 'Preparing your data'
./data/	metadata.tsv	Tab-delimited description of strain (i.e., sample) attributes	See 'Preparing your data'
./config/	include.txt	List of strain names to forcibly include during subsampling and filtering	One strain name per line
./config/	exclude.txt	List of strain names to forcibly exclude during subsampling and filtering	One strain name per line

Output files and directories

Directory	File	Description
./auspice/	buildName.json	Output file for visualization in auspice
./results/	aligned.fasta, sequence-disagnostics.tsv, etc.	Raw results files (dependencies) that are shared across all builds
./results/<buildName>/	tree.nwk, aa_mutations.json, etc.	Raw results files (dependencies) that are specific to a single build
./logs/	.log files	Error messages and other information about the run

Workflow configuration files we might want to customize

Directory	File	Description	Configuration
./my_analyses/<mybuildname>/mybuilds.yaml	Specify and define all the builds you'd like to run	See our customization guide
./my_analyses/<mybuildname>/myconfig.yaml	Analysis configuration file; parameterize your analyses here	See our customization guide
./default_config/	default_config.yaml	Default analysis configuration file	Override these settings in ./my_analyses/.../config.yaml
./default_config/	default_auspice_config.json	Default visualization configuration file	Override these settings in ./my_analyses/.../auspice_config.yaml

Workflow configuration files we don't need to touch

Directory	File	Description	Configuration
./	Snakefile	Entry point for snakemake commands; validates input.	No modification needed
./rules/	builds.smk	Defines rules for running each step in the analysis	Modify your config file, rather than hardcode changes into the snakemake file itself
./envs/	nextstrain.yaml	Specifies computing environment needed to run workflow with the --use-conda flag	No modification needed
./schemas/	config.schema.yaml	Defines format (e.g., required fields and types) for config.yaml files.	Useful reference, but no modification needed.
./scripts/	add_priorities_to_meta.py, etc.	Helper scripts for common tasks	No modification needed