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snakemake

Is it possible in snakemake to produce reports and the DAG images automatically?

I would like to automatically produce the report and DAG images automatically after running the workflow in snakemake. Also I would like to create the report with a given name, e.g. specified in the config.yaml.

I cannot use the snakemake shell command inside the Snakefile which I would usually use to create the reports manually.

The code I would use for creating the report manually:

snakemake --report

The code for manually creating the DAG image:

snakemake --rulegraph | dot -Tpdf > dag.pdf

How can I do this in the Snakefile?

Thanks for any help!

Solution

  • You could do this but it looks pretty ugly to me. At the end of your Snakefile add:

    onsuccess:
    shell(
        r"""
        snakemake --unlock
        snakemake --report
        snakemake --rulegraph | dot -Tpdf > dag.pdf
        """)