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

The files in this repository fall into one of these 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 all of the files one by one, but here are the most important ones for your reference:

• Input files

  • data/metadata.tsv: tab-delimited description of strain (i.e., sample) attributes

  • data/sequences.fasta: genomic sequences whose ids must match the strain column in metadata.tsv. See the data preparation guide.

  • my_profiles/<your_profile>/builds.yaml: workflow configuration file where you can define and parameterize the builds you want to run. The directory name your_profile is the name of your custom analysis profile where you store this configuration and other custom files for the analysis. See the customization guide.

• Output files

  • auspice/<build_name>.json: output file for visualization in Auspice where <build_name> is the name of a build defined in the workflow configuration file.

Input files

• data/metadata.tsv: tab-delimited description of strain (i.e., sample) attributes

• data/sequences.fasta: genomic sequences whose ids must match the strain column in metadata.tsv. See the data preparation guide.

• defaults/include.txt: list of strain names to include during subsampling and filtering (one strain name per line)

• defaults/exclude.txt: list of strain names to exclude during subsampling and filtering (one strain name per line)

Output files and directories

• auspice/<build_name>.json: output file for visualization in Auspice where <build_name> is the name of your build in the workflow configuration file.

• results/aligned.fasta, etc.: raw results files (dependencies) that are shared across all builds.

• results/<build_name>/: raw results files (dependencies) that are specific to a single build.

• logs/: Log files with error messages and other information about the run.

• benchmarks/: Run-times (and memory usage on Linux systems) for each rule in the workflow.

Workflow configuration files we might want to customize

• my_profiles/<your_profile>/builds.yaml: workflow configuration file where you can define and configure all the builds you’d like to run. See the customization guide.

• my_profiles/<your_profile>/config.yaml: Snakemake profile configuration where you can define the number of cores to use at once, etc. See the customization guide.

• defaults/parameters.yaml: default workflow configuration parameters. Override these settings in the workflow configuration file (builds.yaml) above.

• defaults/auspice_config.json: default visualization configuration file. Override these settings in my_profiles/<your_profile>/auspice_config.json. See the customization guide for visualizations.

Workflow configuration files we don’t need to touch

• Snakefile: entry point for Snakemake commands that also validates inputs. No modification needed.

• workflow/snakemake_rules/main_workflow.smk: defines rules for running each step in the analysis. Modify your builds.yaml file, rather than hardcode changes into the snakemake file itself.

• workflow/envs/nextstrain.yaml: specifies computing environment needed to run workflow with the --use-conda flag. No modification needed.

• workflow/schemas/config.schema.yaml: defines format (e.g., required fields and types) for builds.yaml files. This can be a useful reference, but no modification needed.

• scripts/: helper scripts for common tasks. No modification needed.