qc_report() is the high-level floundeR report assembly API. It combines
prepared Grammateus semantic report elements, optional governed figures, and
a Mnemosyne Biosciences theme descriptor into a stable report contract and
manifest. The public package always writes the contract and manifest without
requiring private Grammateus assets. HTML/PDF rendering is attempted only
when requested and an authorized Grammateus runtime is available; otherwise
the manifest records an explicit render status.
Usage
qc_report(
elements,
figures = NULL,
output_dir,
output = c("html", "pdf"),
render = c("if_available", "never", "require"),
theme = grammateus_mnemosyne_theme(),
report_id = "report_nanopore_qc",
title = "Nanopore sequencing QC report",
produced_by = "floundeR",
producer_version = NULL,
produced_at_utc = Sys.time(),
run_id = NULL,
overwrite = TRUE
)Arguments
- elements
A single Grammateus report element, a
flounder_grammateus_report_element_bundle, or a named list of report elements.- figures
Optional governed figure, figure bundle, or list of governed figures prepared by
grammateus_figure_from_file()orgrammateus_figure_from_ggplot().- output_dir
Directory where the report contract and manifest are written.
- output
Requested rendered formats. Use any of
htmlandpdf.- render
Render policy:
if_availablerecords unavailable render outputs when the private runtime is absent,neverwrites only the contract and manifest, andrequireerrors unless rendering is available.- theme
A
flounder_grammateus_themeobject.- report_id
Stable lower-snake-case report identifier. Must start with
report_.- title
Human-readable report title.
- produced_by
Producing software or service name.
- producer_version
Producing software version.
- produced_at_utc
Production timestamp.
- run_id
Optional upstream run, workflow, or analysis identifier.
- overwrite
Whether existing report artifact paths may be replaced.