icgc-argo / song-metadata-integrity-validation

ICGC ARGO RDPC SONG Metadata Integrity Validation

This repository contain scripts to perform integrity validation on metadata recorded in SONG analysis objects. Examples of integrity violation: duplicated alignment results, missing qc_metrics analysis, WXS tumour sequence paired with WGS normal sequence etc.

Create Elasticsearch index for development

Some SONG metadata have been dumped as JSON documents and stored under song-analysis-dump, the following example command load SONG analysis objects from PACA-CA study (also known as program) into an Elasticsearch index called song-2021-05-25, run:

./scripts/indexer.py -i song-2021-05-25 -d song-analysis-dump/PACA-CA.20210507.json song-analysis-dump/PACA-CA.inter.20210512.json

Note: please make sure an Elasticsearch server run at localhost:9200

Run validation

The follow example command generates validation reports for all SONG objects in PACA-CA study.

./scripts/validator.py -i song-2021-05-25 -p PACA-CA

You can report on a particular donor, for example use -d DO230463 to report only for this donor.

This still a WIP, no actual reports yet.