snakemake-staging 0.0.2

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"Staging" for Snakemake

This package provides a mechanism for Snakemake workflows to explicitly "stage out" the output files from certain rules to a public repository like Zenodo to allow faster re-execution of the workflow, using these previously generated artifacts. This can be especially useful for workflows with computationally expensive rules that don't need to be frequently re-run.

snakemake-staging is a spin-off of the showyourwork project, which provides a "caching" framework for Snakemake workflows, to transparently avoid re-execution of rules that have been cached to Zenodo. The implementation of this logic in showyourwork is, however, somewhat fragile and unpredictable. In snakemake-staging, we take a more explicit approach, where "staged" rules are always either explicitly executed or restored.

Installation

To use snakemake-staging in your workflow, you can install it using pip (it's probably best to set up your Snakemake installation following the Snakemake docs first):

python -m pip install snakemake-staging

Quickstart

The Snakefile

While testing, it's probably best to use the Zenodo Sandbox, rather than the main site, since any archive published to Zenodo is permanent. To use the sandbox, you'll need a personal access token stored in the SANDBOX_TOKEN environment variable. You can generate a new token here.

Once you've added this token to your environment, you can edit the Snakefile for your workflow to use snakemake-staging as follows. First, towards the top of your Snakefile, add:

import snakemake_staging as staging

stage = staging.ZenodoStage(
    "zenodo-stage",
    config.get("restore", False)
)

to create a new stage called zenodo-stage. Note that here we're extracting a restore flag from the Snakemake config, which will be used to determine whether to restore files for the stage. This means that you can control the behavior of this stage from the command line. By passing --config restore=True to the snakemake command line interface, all files staged out by the zenodo-stage stage will be restored from the archive rather than generated.

Then, to stage out a rule, you can apply the stage as follows:

rule expensive:
    input:
        ...
    output:
        stage(
            "path/to/output1.txt",
            "path/to/output2.txt",
        )
    shell:
        ...

Finally, after defining all the rules that you want to stage out, you must add the following include which defines all the staging rules:

include: staging.snakefile()

At this point, here's the full Snakefile:

Full Snakefile

import snakemake_staging as staging

stage = staging.ZenodoStage(
    "zenodo-stage",
    config.get("restore", False)
)

rule expensive:
    input:
        ...
    output:
        stage(
            "path/to/output1.txt",
            "path/to/output2.txt",
        )
    shell:
        ...

include: staging.snakefile()

Usage

With the Snakefile defined in the previous section, you can now run your workflow in 3 ways:

1. Normal execution: If you run something like snakemake path/to/output1.txt (where I have omitted the usual --cores and --conda arguments) will execute the workflow as normal, without staging out any files.

2. Stage upload: If you instead have Snakemake target the staging__upload rule, the expensive rule will be executed, and the outputs will be uploaded to Zenodo, saving the record information to zenodo-stage.zenodo.json (this filename can be changed by passing the info_file argument to the ZenodoStage constructor).

3. Stage restore: Finally, after these outputs have been uploaded to Zenodo, you can call Snakemake --config restore=True to disable the expensive rule, and force the outputs to be restored from Zenodo.