Skip to content

Latest commit

 

History

History
54 lines (36 loc) · 2.18 KB

README.md

File metadata and controls

54 lines (36 loc) · 2.18 KB
Raw

Nextflow pipeline for Tools API

A proof-of-concept Tools API service that runs BLAST jobs through Nextflow pipelines.

This repo contains:

  • REST microservice (FastAPI app) with current Tools API endpoints (2020.ensembl.org/api/tools/blast/...)
  • A 4-step NextFlow pipeline for running a BLAST job from submission to processed results file

This repo needs:

  • A task management layer between the nextflow pipeline and the Tools API REST service

NextFlow runs a BLAST job from start to finish, storing all data to files. Tools API needs a way to launch, inspect and manage the pipelines (e.g. to get a BLAST job status from the step 2 of a specific pipeline run). FastAPI currently uses the nextflow python module for this, but it's quite limited and lacks features like a jobs database, track/trace, dashboard, etc.

Setup

  • See the docs to install Nextflow
  • Optional: create Nextflow Tower user account and add its access token to nextflow.config file

Usage

Run the pipeline locally (uses the included BLAST job submission payload):

nextflow run blast_pipeline.nf

Add -with-tower to send the pipeline status to Nextflow Tower dashboard. Add -with-docker to run the pipeline in a container. Nextflow's docker option only includes the pipeline. Needs a custom setup to add nextflow runtime, Tools API server etc.

Run the pipelne through Tools API:

  • Start the REST server (e.g. in python virtualenv):
pip3 install --no-cache-dir -r requirements.txt
uvicorn app.main:app --proxy-headers --host 0.0.0.0 --port 8000

See http://localhost:8000/docs for available endpoints.

  • Start the pipeline (submit a BLAST job to the Tools API REST ednpoint):
curl -H 'Content-Type: application/json' -d @data/blast_payload.json http://localhost:8000/blast/job

Returns submission ID.

  • Get status of the BLAST job: http://localhost:8000/blast/jobs/status/:submission_id
  • Get processed BLAST results file: http://localhost:8000/blast/jobs/result/:submission_id

See blast_pipeline.nf script and Nextflow docs for more details about the pipeline.