Add deployable RNA-seq report portal

Author: Ekin-Kahraman

.github/workflows/ci.yml

@@ -10,14 +10,14 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: actions/setup-java@v4
         with:
           distribution: temurin
           java-version: 21
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 
@@ -53,3 +53,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r cloud/report-portal/requirements.txt
           pytest cloud/report-portal/tests
+
+      - name: Build report portal image
+        run: docker build -t rnaseq-report-portal cloud/report-portal

README.md

@@ -14,6 +14,7 @@ Designed around the [Himes et al. (2014)](https://doi.org/10.1371/journal.pone.0
 - Full synthetic smoke test in GitHub Actions, including containerised FastQC, fastp, HISAT2, samtools, featureCounts, DESeq2 and MultiQC.
 - Docker, Singularity and AWS Batch profiles in `nextflow.config`.
 - Containerised FastAPI report portal under `cloud/report-portal/` for S3-hosted reports and Postgres run metadata.
+- Render Blueprint at `render.yaml` for a deployable FastAPI plus Postgres report portal.
 - `nextflow_schema.json` for parameter discovery in Seqera Platform and other launch tooling.
 - Nextflow execution report, timeline, trace and DAG written to `results/pipeline_info/` on every run.
 - `scripts/validate_outputs.py` checks count matrices, DESeq2 output, plots, MultiQC and run metadata in CI.
@@ -125,14 +126,27 @@ nextflow run Ekin-Kahraman/rnaseq-nextflow-pipeline \
 
 ### Report portal
 
-The optional [cloud report portal](cloud/report-portal/) registers cloud runs and returns signed S3 URLs for Nextflow reports, timelines, traces, DAGs and MultiQC output. It is a small FastAPI service backed by Postgres in production and SQLite for local testing.
+The optional [cloud report portal](cloud/report-portal/) registers cloud runs and returns signed S3 URLs for Nextflow reports, timelines, traces, DAGs and MultiQC output. It is a small FastAPI service backed by Postgres in production and SQLite for local testing. The root route renders a browser dashboard and `/docs` exposes the API.
 
 ```bash
 cd cloud/report-portal
 pip install -r requirements.txt
 uvicorn app.main:app --reload --port 8000
 ```
 
+Run the local Postgres stack:
+
+```bash
+cd cloud/report-portal
+docker compose up --build
+```
+
+Deploy shape:
+
+```text
+render.yaml -> Docker FastAPI service + managed Postgres + S3 presigned report links
+```
+
 ## Parameters
 
 | Parameter | Default | Description |
@@ -169,6 +183,7 @@ results/
 - **Docker and Singularity** - `-profile docker` for local, `-profile singularity` for HPC where Docker is typically unavailable.
 - **AWS Batch profile** - `-profile awsbatch` runs the same containerised workflow on managed cloud compute with S3 work and output paths.
 - **Report portal separated from compute** - Nextflow stays responsible for execution; the FastAPI portal only stores run metadata and signs S3 artefact links, which keeps the cloud proof small and auditable.
+- **Render Blueprint** - `render.yaml` defines the web service, managed Postgres database, demo seed run and AWS secret placeholders as reviewable infrastructure-as-code.
 - **Run metadata by default** - Nextflow report, timeline, trace and DAG are emitted on every run so failures and performance can be audited after the fact.
 - **Reverse-stranded default** - `--strandedness 2` because the airway dataset (and most modern Illumina dUTP protocols) produces reverse-stranded libraries. Users with older unstranded preps should set `--strandedness 0`.
 - **Configurable contrast** - `--ref_condition` sets the DESeq2 reference level. Defaults to "untreated" for the airway dataset.
@@ -178,7 +193,7 @@ results/
 
 - **2 samples per condition in the demo** - underpowered for reliable DE. The DESeq2 step runs and produces output, but with n=2 the results are illustrative, not statistically robust. Proper analysis requires ≥3 replicates per condition.
 - **CI uses synthetic data** - the public CI proves the full software path, not the biological conclusion. Real Himes/GSE52778 runs require external FASTQs, GRCh38 HISAT2 index and Gencode annotation files.
-- **AWS Batch proof status** - the profile and report portal are implemented, but no public real AWS Batch run artefact is committed yet.
+- **AWS Batch proof status** - the profile and report portal are implemented, but no public real AWS Batch run artefact is committed yet. The report portal is the current cloud proof path until a real Batch run is published.
 - **No STAR option** - only HISAT2 is implemented. Adding STAR as an alternative aligner would allow benchmarking on the same data.
 
 ## Licence

cloud/report-portal/.dockerignore

@@ -0,0 +1,7 @@
+.venv/
+__pycache__/
+*.pyc
+*.db
+*.sqlite
+.pytest_cache/
+tests/

cloud/report-portal/Dockerfile

@@ -12,4 +12,4 @@ COPY app ./app
 
 EXPOSE 8000
 
-CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["sh", "-c", "uvicorn app.main:app --host 0.0.0.0 --port ${PORT:-8000}"]

cloud/report-portal/README.md

@@ -4,6 +4,8 @@ Small FastAPI service for registering cloud RNA-seq runs and serving signed link
 
 This is intentionally separate from the Nextflow pipeline. The pipeline remains responsible for compute and published artefacts; the portal gives reviewers and collaborators a minimal cloud-facing surface for run status and report access.
 
+The root route renders a small dashboard for browser review. The API remains available through `/docs`, `/runs` and `/runs/{id}/artifacts`.
+
 ## Architecture
 
 ```text
@@ -25,6 +27,8 @@ Nextflow AWS Batch run
 | `DATABASE_URL` | `postgresql+psycopg://rnaseq:change_me@db:5432/rnaseq` | Metadata database. Defaults to local SQLite for development. |
 | `AWS_REGION` | `eu-west-2` | Region used by the AWS SDK. |
 | AWS credentials | IAM role, env vars, or workload identity | Required only for signed S3 URLs. |
+| `DEMO_RUN_ID` | `synthetic-ci-001` | Optional seed run for live demos. |
+| `DEMO_S3_PREFIX` | `s3://bucket/results/synthetic-ci-001` | Optional S3 prefix for the seeded demo run. |
 
 ## Local Smoke Run
 
@@ -35,6 +39,8 @@ pip install -r requirements.txt
 uvicorn app.main:app --reload --port 8000
 ```
 
+Open <http://localhost:8000> for the dashboard or <http://localhost:8000/docs> for the OpenAPI UI.
+
 Register a completed run:
 
 ```bash
@@ -63,6 +69,29 @@ docker run --rm -p 8000:8000 \
   rnaseq-report-portal
 ```
 
+Run the full local stack with Postgres:
+
+```bash
+docker compose up --build
+```
+
+The compose stack seeds a synthetic run so the dashboard has a visible record immediately.
+
+## Render Blueprint
+
+The repository root contains `render.yaml` for a reproducible Render deployment:
+
+- Docker web service built from `cloud/report-portal/Dockerfile`.
+- Managed Postgres database connected through `DATABASE_URL`.
+- Optional demo run seeded through `DEMO_RUN_ID` and `DEMO_S3_PREFIX`.
+- AWS credentials stored as Dashboard secrets for S3 presigned URLs.
+
+Open the Blueprint after the file is pushed:
+
+```text
+https://dashboard.render.com/blueprint/new?repo=https://github.com/Ekin-Kahraman/rnaseq-nextflow-pipeline
+```
+
 ## Tests
 
 ```bash