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Washington MPXV Build

This Nextstrain build follows the structure detailed in the Pathogen Repo Guide.

This description highlights those files and their role in the Washington MPXV build.

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Directory structure

├── README.md
├── Snakefile
├── .snakemake
├── auspice
├── bin
├── build-configs
├── data
├── defaults
├── example_data
├── logs
├── profiles
├── results
├── rules
└── scripts
├── wa_mpxv

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Folder descriptions

The MPXV wiki page provides an in-depth overview of several key folders with this repo.

• Snakefile: A Snakefile is a key component of the Snakemake workflow management system, serving as the blueprint for defining and organizing data processing workflows. It is a plain text file that contains a series of rules, each specifying how to transform input files into output files.
• .snakemake/: This folder is created by the Snakemake workflow management system and contains important components that assist in the execution and management of data workflows. The contents help manage the workflow's execution efficiently, ensuring reproducibility and tracking changes throughout the data processing pipeline.
• bin/: Inert files that outline Slack tokens that alert users on Slack of when the build is starting, if an error occurs, where it is being deployed and if it was successful.
• build-configs/: Inert files and folders that have been included for automating Nextstrain builds.
• data/: Contains ingested compressed metadata and sequences folders that are then decompressed into their respected .tsv and .fasta files.
• defaults/: Folder contains default parameters for the build.
• example_data/: Folder containing example data for testing out a build run.
• logs/: A folder created by Snakemake that is used to store log files that capture detailed information about the execution of the workflow. This folder is essential for monitoring, debugging, and optimizing workflow runs.
• profiles/: This folder is created by Snakemake and is vital for organizing and managing environment-specific configurations, enabling users to run workflows efficiently and consistently across different computing setups. It enhances the flexibility and usability of Snakemake, particularly in multi-user environments or when transitioning between local and distributed computing resources.
• rules/: This folder is created by Snakemake and is a dedicated directory for rule definitions relating to your workflow.
• scripts/: This folder contains Python scripts dedicated to the workflow.
• wa_mpxv/: Folder containing the workflow for building a Washington focused MPXV Clade IIb build.
• bin/: Inert files that outline Slack tokens that alert users on Slack of when the build is starting, if an error occurs, where it is being deployed and if it was successful.
• build-configs/: Inert files and folders that have been included for automating Nextstrain builds.
• data/: Contains ingested compressed metadata and sequences folders that are then decompressed into their respected .tsv and .fasta files.
• defaults/: Folder contains default parameters.
• example_data/: Folder containing example data for testing out a build run.
• logs/: A folder created by Snakemake that is used to store log files that capture detailed information about the execution of the workflow. This folder is essential for monitoring, debugging, and optimizing workflow runs.
• profiles/: This folder is created by Snakemake and is vital for organizing and managing environment-specific configurations, enabling users to run workflows efficiently and consistently across different computing setups. It enhances the flexibility and usability of Snakemake, particularly in multi-user environments or when transitioning between local and distributed computing resources.
• rules/: This folder is created by Snakemake and is a dedicated directory for rule definitions relating to your workflow.
• scripts/: This folder contains Python scripts dedicated to the workflow.
• wa_mpxv/: Folder containing the workflow for building a Washington focused MPXV Clade IIb build.