annotate_doc
annotate_doc writes the documentation of an annotation pipeline. It
reads a pipeline, a YAML file or a GRR pipeline resource id, and the GRR
definition that resolves the resources of the pipeline. It writes an HTML
page that describes the annotators of the pipeline and the attributes that
they produce. Use it to review a pipeline before you annotate with it, or to
share a description of a pipeline. Without -o, the tool prints the HTML
page to the standard output.
Examples
annotate_doc custom_pipeline.yaml > doc.html
Writes the documentation of a pipeline file to doc.html.
annotate_doc pipeline/hg38_clinical_annotation -o hg38_clinical_annotation.html
Writes the documentation of a pipeline resource of the GRR to
hg38_clinical_annotation.html.
See also
Custom annotation pipelines: review the attributes of a custom pipeline.
annotate_doc: an example of the page and the common options.
Option reference
The tool also accepts the pipeline argument and the GRR context options
-g, --grr-directory, -R, -G and -ar. The
annotate_tabular option reference describes
them.
usage: annotate_doc [-h] [-o OUTPUT] [--verbose] [--logfile LOGFILE]
Named Arguments
- -o, --output
The name of the output HTML file. Without this option, the tool prints the HTML page to the standard output.
- --verbose, -v, -V
Default:
0- --logfile
File to log output to. If not set, logs to console.