Snakemake storage plugin: fs

Warning

No documentation found in repository https://github.com/snakemake/snakemake-storage-plugin-fs. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instructions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-storage-plugin-fs
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Usage

Queries

Queries to this storage should have the following format:

Query type	Query	Description
any	test/test.txt	Some file or directory path.

As default provider

If you want all your input and output (which is not explicitly marked to come from another storage) to be written to and read from this storage, you can use it as a default provider via:

snakemake --default-storage-provider fs --default-storage-prefix ...
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with ... being the prefix of a query under which you want to store all your results.

Within the workflow

If you want to use this storage plugin only for specific items, you can register it inside of your workflow:

# register storage provider (not needed if no custom settings are to be defined here)
storage:
    provider="fs",

rule example:
    input:
        storage.fs(
            # define query to the storage backend here
            ...
        ),
    output:
        "example.txt"
    shell:
        "..."
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