Integration with workflow management systems

Snakemake

Datavzrd integrates easily into any Snakemake workflow by using its own wrapper.

Snakemake’s datavzrd wrapper can be used in the following way:

rule datavzrd:
    input:
        # the config file may be a yte template, with access to input, params and wildcards
        # analogous to Snakemake's generic template support:
        # https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#template-rendering-integration
        # For template processing, __use_yte__: true has to be stated in the config file
        config="resources/{sample}.datavzrd.yaml",
        # optional files required for rendering the given config
        table="data/{sample}.tsv",
    params:
        extra="",
    output:
        report(
            directory("results/datavzrd-report/{sample}"),
            htmlindex="index.html",
            # see https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html
            # for additional options like caption, categories and labels
        ),
    log:
        "logs/datavzrd_report/{sample}.log",
    wrapper:
        "v3.13.4/utils/datavzrd"

Importantly, the report() marker instructs Snakemake to embed the Datavzrd report into the Snakemake report. This way, Datavzrd’s interative exploration capabilities are further enriched by the data provenance and reproducibility information as well as the result navigation features available in Snakemake reports.

Nextflow

Datavzrd is available as an nf‑core module for inclusion in Nextflow pipelines. It can be installed via:

nf-core modules install datavzrd