Analysis workflow tracking and quality control dashboard - seqcode/pegr GitHub Wiki

Under the "Sequencing Report" -> "Sequencing Runs" tab, the table has a column named "Run Analysis Status". The "Details" links will take you to the analysis workflow tracking and quality control dashboard.

As the output data from each analysis step returns to PEGR individually, the status of the workflow is updated in realtime. The status of each analysis step is represented by a square. If the output returns successfully and passes the preliminary validation, the square will be colored in green. The output that has one or more error messages are colored in red and clicking on the square will render the detailed error messages. API calls with permission de- nied are colored in orange, and analysis steps with missing datasets are labeled in blue. The analysis steps that have not returned output will remain in grey. If all squares become green, it indicates that the entire workflow has completed successfully.

Different workflows are displayed in separate tabs. Each workflow tab can have a customized set of columns. And the configuration can be defined in Admin -> Alignment and Analysis -> Pipeline. The "Workflow id" should match that received from "stats" API calls. And the "Steps" should be a list of step and category pair, e.g. "[["step1", "category1"], ...]".

The quality control panel lists the number of requested tags and the major statistics of the sequencing results, including total reads, adapter dimers, mapped reads, uniquely mapped reads and duplication level. The acceptable range of each field is indicated at the header and fields that have values outside the acceptable ranges are colored in red. The combination of the statistics gives users an overview of the quality of the sequencing experiment. After reviewing the statistics, authorized users can indicate if the sample has passed the quality control check and been "verified". If the statistics indicates that the sequencing result is incorrect, the user can "delete" the sample directly on this page.

Users can hide unwanted columns by clicking the "-" sign on the header. The columns can be restored by clicking the "+" sign at the top.