The Covid Workflow Manager contains pipelines and services that run processing pipelines for the SARS-CoV-2 Data Hubs, as part of the European COVID-19 Data Platform.
| Pipeline | Location | Description |
|---|---|---|
| Jovian | /jovian |
A user-friendly Viromics toolkit |
| Artic | /artic |
nCoV-2019 novel coronavirus bioinformatics protocol |
| ENA Nanopore | /ont |
A customised pipeline for analysing Nanopore SARS-CoV-2 data |
| ENA SARS-CoV2 Variant Calling | /vcf |
A pipeline for mapping, calling, and annotation of SARS-CoV2 variants |
| Service | Location | Description |
|---|---|---|
| Pangolin | /pangolin |
Lineage annotation service |
| Reports | /reports |
Interactive reporting and analysis services |
| Logs | /logs |
Logging dashboard that displays the status of pipeline runs |