Scalable, reproducible bioinformatics workflows using Nextflow & nf-core

Alexander Peltzer

 

ELIXIR Workshop on FAIR Computational Workflows

September 2, 2020

Dataflow Model

 

Domain-specific language

Executor abstraction

 

Tools

Guidelines

Pipelines

A community effort to collect a curated set of analysis pipelines built using Nextflow.

  • 25 stable
  • 15 in development

Github Actions: CI Testing

Linting

$ cd path/to/my_pipeline
$ nf-core lint .

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'
    nf-core/tools version 1.10.dev0


  INFO     Testing pipeline: nf-core-testpipeline/
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 3 Test Warnings                                                                                      │
├──────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ https://nf-co.re/errors#5: GitHub Actions AWS full test should test full datasets: nf-core-testpipeline… │
│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::fastqc=0.11.8, 0.11.9 avail… │
│ https://nf-co.re/errors#8: Conda package is not latest available: bioconda::multiqc=1.7, 1.9 available   │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 117 Tests Passed  │
│ [!]   3 Test Warnings │
│ [✗]   0 Test Failed   │
╰───────────────────────╯

JSON Schema

JSON Schema

JSON Schema

Nextflow Tower

AWS Megatests

FAIRification of nf-core

Dockstore (supported)

ro-crate (prototyping)

Evaluating

JSON Schema

ECCB2020 NXF + NF-Core

By Alexander Peltzer

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