Build and write Synoptikon QC payloads — as_synoptikon

as_synoptikon_qc() assembles existing floundeR QC evidence into the versioned Synoptikon payload contract installed at inst/schema/synoptikon-qc-payload-v1.schema.json. write_synoptikon_qc() writes that payload as JSON.

Usage

as_synoptikon_qc(
  run_summary = NULL,
  report_cards = NULL,
  sequencing_summary = NULL,
  flowcell = NULL,
  barcode = NULL,
  pod5 = NULL,
  bam = NULL,
  library_preparation = NULL,
  input_provenance = list(),
  run_identity = list(),
  governance_context = list(),
  payload_id = NULL,
  generated_at_utc = Sys.time(),
  limitations = list(),
  intended_use = c("qc_ingestion", "review", "reporting"),
  compatible_with_grammateus_trusted_reports = TRUE
)

write_synoptikon_qc(path, ..., pretty = TRUE)

Arguments

run_summary: Optional qc_run_summary() one-row tibble.
report_cards: Optional report-card tibble, list of report-card tibbles, or already wrapped report-card list.
sequencing_summary, flowcell, barcode, pod5, bam, library_preparation: Optional section evidence. Each may be a data frame/tibble or a named list of data frames/tibbles.
input_provenance: List of input provenance records.
run_identity: Named list of run, sample, project, flow-cell, kit, and instrument identifiers.
governance_context: Named list of Synoptikon/Mneion governance identifiers.
payload_id: Stable payload identifier. When omitted, a timestamped identifier is generated.
generated_at_utc: Production timestamp as POSIXct or ISO-8601 string.
limitations: List of limitation records.
intended_use: Character vector of Synoptikon intended-use labels.
compatible_with_grammateus_trusted_reports: Logical compatibility flag.
path: Output JSON file path for write_synoptikon_qc().
...: Passed from write_synoptikon_qc() to as_synoptikon_qc().
pretty: Whether to pretty-print JSON.

Value

as_synoptikon_qc() returns a named list compatible with the v1 Synoptikon QC payload schema. write_synoptikon_qc() returns path invisibly after writing JSON.

Examples

summary_file <- flnDr("sequencing_summary.txt.bz2")
payload <- as_synoptikon_qc(
  run_summary = qc_run_summary(summary_file),
  report_cards = qc_report_card(summary_file),
  payload_id = "example-qc-payload"
)