Possible Pure Python SnakeMake API

snaker.py

from snakemake.core import SnakeMakeShellRule, SnakeMakePyRule, AllRule


class CollectReferences(SnakeMakeShellRule):
    ID = "collect_references"
    THREADS = 8
    DESCRIPTION = "Does some stuff"

    def inputs():
        return dict(alpha="f1.fasta")

    def resolve_params(config):
        return dict(a=1, b=2)

    def outputs():
        return dict(gamma="out1.txt", delta="out2.txt")

    def shell(inputs, outputs, config):
        return "run-my-exe {config.nthreads} {inputs.alpha} {outs.gamma}"


class SubreadSetSummary(SnakeMakePyRule):
    ID = "subreads_summary"
    DESCRIPTION = "Create a txt summary of SubreadSet XML"

    def inputs():
        return dict(s1="/path/to/subreadset.xml")

    def outputs():
        return dict(summary="summary.txt")

    def run(inputs, outputs, config):
        from pbcore.dataset.io import SubreadSet

        s = SubreadSet(inputs.s1)
        with open(outputs.summary, 'w+') as f:
            f.write(repr(s))
        return 0


class CustomSummaryWorkflow(AllRule):
    INPUTS = dict(
        s1="summary.txt",
        gamma="out1.txt",
        delta="outs2.txt")

    DEFAULT_PARAMS = dict(a=1, b=2)