Reproducible data analysis with Nextflow & NF-core

 

Alexander Peltzer

Quantitative Biology Center (QBiC) Tübingen

http://bit.ly/nfcoreisc2018

Outlook

 

  • Challenges in computational biology
  • Basic principles of Nextflow
  • Introduction to NF-core project

Challenges: Big Data

 

  • Data in computational biology is
    • big (PB scale)
    • diverse (sequencing, proteomics, metabolomics ...)
    • erroneous (e.g. contains sequencing errors)

 

 

We need methods and tools to analyze such data!

Challenges: Big Data - ICGC

Text

"Hyper-Moore gap"

Text

Credit to Swaine Chen, Genome Institute of Singapore, AWS Summit 2018

The FAIR* principle

 

Findable

Accessible

Interoperable

Reproducible

 

 

 

The FAIR Guiding Principles for scientific data management and stewardship, Wilkinson et al. 2016 qPortal: A platform for data-driven biomedical research, Mohr et al. 2018

 

 

DOI

qPortal

?

?

 

 

 

 

Challenges: Software dependencies

 

 

Workflows / Pipelines consist of

  • different tools
  • dozens of individual methods

 

Complex dependency trees and configuration requirements!

 

Steinbiss et al., "Companion: a web server for annotation and analysis of parasite genomes", NAR 2016

Challenges: Reproducibility

 

  • Large-scale projects more common today
    • 1,000 Genomes Project
    • 100,000 Genomes Project UK
  • Reproduce results with older data / integrate with newer data
  • Challenging: Many paper results are not reproducible at all or require a lot of effort

 

Challenges: Reproducibility

 

"We estimated the overall time to reproduce the method as 280 hours for a novice with minimal expertise in bioinformatics."

Challenges: Environmental stability

 

 

 

  • Portability and stability of code between different OS should be ensured
  • Are results different? Yes, they are ...

 

Challenges: Software dependencies

 

 

diTommaso et al., 2017, Nature Biotechnology

Nextflow

 

  • Custom DSL (domain-specific language) for
    • fast prototyping
    • enabling task composition
    • easy parallelization
  • Self-contained: Containerize tasks (e.g. with Docker)
  • Isolation of dependencies: Keep container - rerun analysis at any point!

(credit to E Floden, CRG Barcelona)

Nextflow: Centralised Orchestration

 

Nextflow

Cluster

  • Submit jobs to cluster nodes
  • Store data on shared storage

Storage

Nextflow: Cloud deployment (AWS)

 

(credit to E Floden, CRG Barcelona)

Platform support

(credit to E Floden, CRG Barcelona)

Nextflow: Executor abstraction

 

Improves code portability

#Run me locally
process.executor = 'local'

#Run on AWS Batch
process.executor = 'awsbatch'

#Run on Kubernetes cluster
process.executor = 'k8s'
  • Community effort to collect production ready analysis pipelines
  • Save time in development, more testing, more updates
  • https://nf-co.re

 

Phil Ewels

Alex Peltzer

Sven Fillinger

Andreas Wilm

Maxime Garcia

+ many others!

Tiffany Delhomme

  • Community effort to collect production ready analysis pipelines
  • Save time in development, more testing, more updates
  • Initially supported by SciLifeLab, QBiC and A*Star Genome Institute Singapore

 

All pipelines adhere to requirements

  • Nextflow based
  • MIT license
  • Software bundled in Docker
  • Continuous integration testing (e.g. Travis CI)
  • Stable release tags
  • Common pipeline usage and structure

Dockerfiles

FROM nfcore/base
MAINTAINER Phil Ewels <phil.ewels@scilifelab.se>
LABEL authors="phil.ewels@scilifelab.se" \
    description="Docker image containing all requirements for the nfcore/rnaseq pipeline"

COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nfcore-rnaseq-1.5dev/bin:$PATH

Dockerfiles

  • Bioconda package based, clean-style
name: nfcore-rnaseq-1.5dev
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - conda-forge::openjdk=8.0.144
  - fastqc=0.11.7
  - trim-galore=0.4.5
  - star=2.6.0c
  - hisat2=2.1.0
  - picard=2.18.7
  - bioconductor-dupradar=1.8.0
  - conda-forge::r-data.table=1.11.4
  - conda-forge::r-gplots=3.0.1
  - bioconductor-edger=3.20.7
  - conda-forge::r-markdown=0.8
  - preseq=2.0.3
  - rseqc=2.6.4
  - samtools=1.8
  - stringtie=1.3.4
  - subread=1.6.1
  - multiqc=1.5

Optional requirements

 

  • Software bundled in bioconda
  • Optimised output formats (e.g. CRAM)
  • Explicit support for cloud environments (AWS)
  • Benchmarks for running on such environments

Need help?

 

  • Cookiecutter: To get a skeleton for new pipelines
  • Linting app: To check what conforms with nf-co.re
  • Gitter: To communicate with the community!

 

It's demo time!

https://asciinema.org/a/2vhoPGGJLte5EZiGAA1hF9DID

Comes with interactive reports!

Comes with proper documentation!

... and a lot more!

Acknowledgements

Phil Ewels (SciLifeLab)

Maxime Garcia (SciLifeLab)

Sven Fillinger (QBiC)

Paolo di Tommaso (CRG)

Evan Floden (CRG)

Andreas Wilm (A* Singapore)

 

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