ro-crate_snakemake_tooling

Collection of python tools for processing snakemake metadata for RO-Crate creation

Snakemake reporter plugin

Documentation how the wrroc reporter plugin is built.

Setup poetry

Poetry is used for setting up a new plugin from a template.
In my experience, the Python version used here has to match the Python version used with Snakemake environment, otherwise the plugin does not work.
But this should be a solvable problem.

conda create --name poetry python=3.12
conda activate poetry
pip install poetry

Create new plugin from the template

Note: The poetry project was added to this repository.
You only have to install the poetry plugin and can use the project in this repository.

# Install poetry plugin via
poetry self add poetry-snakemake-plugin

# Create a new poetry project via
poetry new snakemake-report-plugin-wrroc

cd snakemake-report-plugin-wrroc

# Scaffold the project as a snakemake report plugin
poetry scaffold-snakemake-report-plugin

# Next, edit the scaffolded code according to your needs, and publish
# the resulting plugin into a github repository. The scaffold command also 
# creates github actions workflows that will immediately start to check and test
# the plugin.

Implement plugin

Implement the report render method here:

snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py

For plugin development one can take a look what information the base class ReporterBase provides.

Build and install plugin

Build wheel and tar.gz:

poetry build

Install the plugin.

pip install --force-reinstall dist/snakemake_report_plugin_wrroc-0.1.0-py3-none-any.whl

Snakemake should find the plugin! Note that there are many copy&paste errors for the reporter plugin, even in the poetry template repository. Most of the time the term executor plugin is used instead of reporter plugin.

snakemake -h
[...]
wrroc executor settings:
  --report-wrroc-myparam VALUE
                        Some help text (default: <dataclasses._MISSING_TYPE object at 0x7f0091b3f140>)

Create a report

Test the reporter plugin in the skim2mt directory, where the .snakemake/metadata resides:

snakemake --reporter wrroc