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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Specify output-format on CLI #471

Closed julesjacobsen closed 1 year ago

julesjacobsen commented 1 year ago

As of 13.1.0 a user can only specify the desired output formats from withing an output-options.yml file or just accept the default HTML and JSON outputs. This isn't very convenient so as a user I would like to be able to specify the desired output formats directly via the command line.

e.g.

java -jar exomiser.cli.jar --sample ... --output-format TSV_VARIANT,TSV_GENE

The cli option:

     --output-format=<outputFormats>[,<outputFormats>...]
                          A list of comma separated output format(s) e.g. HTML or HTML,JSON. Valid options include [HTML, JSON, TSV_GENE, TSV_VARIANT, VCF]. Note that HTML is the most human-friendly, JSON is the
                            most detailed. (default = HTML,JSON)

These options should override any options provided in an old-style analysis.yaml or separate output-options.yaml file.