-
Notifications
You must be signed in to change notification settings - Fork 2
IGO LIMS REST API
The endpoints retrieve patient metadata, IGO processing information, sequencer run information and fastq paths.
Swagger lists the available endpoints and all fields returned, the data team can supply account information to access the endpoints.
During the post-sequencing IGO QC process prior to delivery, entire sequencer runs are archived that may have fastqs that both passed and failed QC. One important aspect to retrieving fastq information from the endpoint is that no failed fastqs are returned by the endpoints.
The LIMS resets nightly so the endpoints will be unavailable for a few minutes, currently from 2:30am-2:35am, also periodically to install updates the endpoints will be down for up to 20 minutes.
Of particular importance to pipeline analysis is when IGO QC recommendation is to fail a sample but the investigator decides to proceed with sequencing.
In February of 2020, four IGO QC fields were added to /api/getSampleManifest, a failed sample is shown below with the IGO Recommendation, comments and then the investigator decision.
"qcReports": [ { "qcReportType": "LIBRARY", "IGORecommendation": "Failed", "comments": "Low quantity", "investigatorDecision": "Stop processing at this time" }
It is possible that IGO will on rare occasions deliver the same project multiple times adding runs and fastqs. In these cases the /api/getDeliveries endpoint will only list each request one time with the most recent delivery date, prior delivery dates are not retrievable from the endpoint.
Since 2019 IGO does three types of RNASeq projects: RNASeq-TruSeqRiboDeplete,RNASeq-TruSeqPolyA and RNASeq-SMARTerAmp for these three types of projects only the endpoints report strand(non-stranded:SMARTerAmp or stranded-reverse:both TruSeq) & LibraryType fields. For historical projects prior to 2019 such as RNASeq-TruSeqFusion strand results in the endpoint are not reliable.