snakemake-report-plugin-nanopub 0.3.0

Reporter plugin for Snakemake using nanopub-py to create workflow metadata nanopubs

Please note: This plugin is work in progress and NOT ready to use.

Its intention:

• users will be enabled to automatically create a nanopub using a workflow's metadata
• this nanopub can subsequently be referenced in publications and thereby covering all metadata necessary to scrutinize an analysis (all too often crucial data are missing from publications)

CLI: plot nanopub knowledge graph

After installation, run:

plot-nanopub-knowledge-graph \
	--dataset-nanopub-id <dataset_nanopub_url> \
	--workflow-nanopub-id <workflow_nanopub_url> \
	--workflow-configuration-id <workflow_configuration_nanopub_url> \
	--report-nanopub-id <report_nanopub_url> \
	-o graph.png

This generates a Graphviz plot with four rounded boxes (Dataset, Workflow, Workflow Configuration, Workflow Report) and arrows labeled used by, used this configuration, produces, and based upon.

Optional settings:

• --line-color "dark brick red" (default) for node border and arrow color
• --format svg|png|pdf to override output format
• --verbose to print debug logs for nanopub description extraction
• --text-width 60 to control line wrapping width in box text

When the output format resolves to svg (via --format svg or an .svg output filename), Graphviz is invoked with svg:cairo so text is embedded as vector outlines. This avoids downstream font substitution/reflow issues during JOSS LuaLaTeX typesetting.

Default output format is png.