The Snakedeploy API

These sections detail the internal functions for Snakedeploy.

snakedeploy.deploy module

snakedeploy.deploy.deploy(source_url: str, name: str | None, tag: str | None, branch: str | None, dest_path: Path, force=False)

Deploy a given workflow to the local machine, using the Snakemake module system.

Example

Given that you want to deploy a workflow to the path /tmp/dest:

from snakedeploy.deploy import deploy
deploy(
    "https://github.com/snakemake-workflows/dna-seq-varlociraptor",
    dest_path="/tmp/dest",
    name="dna_seq",
    tag="v1.0.0",
    force=True
)

snakedeploy.collect_files module

class snakedeploy.collect_files.Match(rule, match)

match

Alias for field number 1

rule

Alias for field number 0

snakedeploy.collect_files.collect_files(config_sheet_path: str)

Given a configuration sheet path with input patterns, print matches of samples to STDOUT