Workflows in Seqera
These pages document how CIFR deploys and runs external or upstream Nextflow pipelines in Seqera Platform.
Why this exists:
- Some repositories under
ncsu-decifrare cloned/forked upstream projects. - Upstream docs often describe implementation; CIFR users need deployment/run instructions in our environment.
- We keep a stable “how to run it here” guide and link to upstream for source details.
Conventions
For each workflow page:
- Upstream repo + branch/tag we deploy
- Seqera pipeline name and workspace
- Profiles/config used (HPC vs local)
- Required inputs (samplesheets, fastqs, refs)
- Outputs and where to find them
- Common failure modes and fixes
Screenshots
Put screenshots in docs/workflows/assets/ and reference them relatively (e.g., assets/run-params.png).