README.md

Nix/Guix Snakemake Wrapper

Snakemake wrapper to simplify the use of Nix and Guix

Nix

The Nix wrapper requires:

• params.flake to know which shell to use

• params.shell for the command to execute

rule test:
    input:
        "flake.nix",
        "flake.lock",
        script="run.py"
    output:
        "test_{i}"
    params:
        flake = ".#pyshell",
        shell = lambda wildcards, input, output: f"python3 {input.script} {wildcards.i} > {output}"
    wrapper:
        "https://github.com/Nix4Science/snakemake-wrapper/raw/0.1.0/nix"

To simplify the transition from a classical Snakefile to a Snakefile using this wrapper, we extend the params.shell to do the evaluation inside the wrapper. If you define the string of params.shell as bytes, the wrapper will evaluate the string itself. So the following is exactly the same as above:

# ...
    params:
        shell = b"python3 {input.script} {wildcards.i} > {output}"
# ...

Guix

The Guix wrapper requires:

• input.manifest for the manifest of the environment

• input.channels for the description of the channels to use

• params.shell for the command to execute

Optional parameters:

• params.container to run the shell with the --container option

rule test_guix:
    input:
        channels="channels.scm",
        manifest="manifest.scm",
        script="run.py"
    output:
        "test_{i}"
    params:
        container=True,
        shell = b"python3 {input.script} {wildcards.i} > {output}"
    wrapper:
        "https://github.com/Nix4Science/snakemake-wrapper/raw/0.1.0/guix"

To simplify the transition from a classical Snakefile to a Snakefile using this wrapper, we extend the params.shell to do the evaluation inside the wrapper. If you define the string of params.shell as bytes, the wrapper will evaluate the string itself. So the following is exactly the same as above:

# ...
    params:
        shell = b"python3 {input.script} {wildcards.i} > {output}"
# ...