ingest: Add summary QC columns `QC_overall_score` and `QC_overall_status` to defaults

[j23414]

Context

While fine-tuning a PRRSV Nextclade dataset, I noticed that the QC summary fields qc.overallScore (numeric) and qc.overallStatus (good / mediocre / bad) are not added by default in the ingest pipelines.

As far as I can tell, these fields provide a concise, high-level summary of confidence in a Nextclade assignment, and are generally useful for downstream filtering and interpretation.

Description

QC summary fields should be available by default in ingested Nextclade outputs, alongside other QC metrics.

Possible solution

Mainly add the following mappings to the default Nextclade ingest config:

    qc.overallScore: "QC_overall_score"
    qc.overallStatus: "QC_overall_status"

Specifically, in:

pathogen-repo-guide/ingest/defaults/nextclade_config.yaml

Lines 11 to 23 in e42caed

	field_map:
	seqName: "seqName"
	clade: "clade"
	coverage: "coverage"
	totalMissing: "missing_data"
	totalSubstitutions: "divergence"
	totalNonACGTNs: "nonACGTN"
	qc.missingData.status: "QC_missing_data"
	qc.mixedSites.status: "QC_mixed_sites"
	qc.privateMutations.status: "QC_rare_mutations"
	qc.frameShifts.status: "QC_frame_shifts"
	qc.stopCodons.status: "QC_stop_codons"
	frameShifts: "frame_shifts"