Slides introducing nf-core to the FAANG community

1. : A community-driven collection
of omics portable pipelines
Jose Espinosa-Carrasco (CRG)
FAANG Shared Workshop – Wellcome Genome Campus, Hinxton, UK
26th
February 2020
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 815668
Disclaimer: the sole responsibility of this presentation lies with the authors. The Research Executive Agency is not responsible for any use that may be made of the information contained therein.

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What is nf-core?
A community effort to collect a curated set of analysis pipelines built using Nextflow.
A set of standardised omics pipelines (ready to use)
A community
Helper tools (users/developers)
Best practice guidelines

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https://nf-core.re/

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Community
https://github.com/nf-core/
https://nf-co.re/join/slack
https://groups.google.com/forum/#!forum/nf-core
https://twitter.com/nf_core
https://www.youtube.com/c/nf-core

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Community: some figures

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Community: some figures

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Community: some figures

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Community: some figures

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Community: some figures

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21 RELEASED
16 UNDER DEVELOPMENT
2 ARCHIVED
39 PIPELINES
A set of standardised omics pipelines

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Some of the pipelines released
atacseq
chipseq
deepvariant
hic
methylseq
rnafusion
rnaseq
scrnaseq

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Build using nextflow
Have a MIT license
Software bundled using Docker/Singularity
CI testing (include minimal test dataset)
Pass nf-core lint tests
Stable release tags (GitHub releases with associated changelog, and DOI using Zenodo)
Common pipeline structure and usage
Run in a single command (pipelines should not be split into multiple sub-pipelines)
Comprehensive documentation
A responsible point of contact
Pipelines nf-core requirements and recommendations
Software bundled with Bioconda (package the software using Bioconda if not already available)
Explicit support for cloud environment
Benchmarks from running on cloud environments
Optimized output file formats (Standard format where possible, including CRAM)

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Software bundled with Bioconda
env.yml
name: rnaseq-nf
channels:
- defaults
- bioconda
- conda-forge
dependencies:
# Default bismark
- salmon=1.0.0
- fastqc=0.11.5
- multiqc=1.5
FROM continuumio/miniconda:4.7.12
MAINTAINER Jose
Espinosa-Carrasco<espinosacarrascoj@gmail.com
>
COPY conda.yml .
RUN
conda env update -n root -f env.yml
&& conda clean -a
Dockerfile

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But how can I run a nf-core pipeline?
Software required
OR
OR
nextflow run nf-core/rnaseq -r 1.4

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Helper tools
pip install nf-core
conda install -c bioconda nf-core

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Helper tools
nf-core --help

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Helper tools (users)
nf-core --list

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But how can I run a nf-core pipeline?
Commands
nf-core launch nf-core/rnaseq

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Config profiles
A default 'base' config (always loaded)
Core profiles (eg. docker, conda, test)
Server profiles (nf-core/configs)
*Once added are immediately available in all pipelines
Your local config files (eg. using the -c flag)

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Config profiles example using test data
nextflow run nf-core/rnaseq -profile test,docker

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Want more?
https://nf-co.re/usage/nf_core_tutorial
nf-core create - Create a new workflow using the nf-core template
nf-core bump version - Update nf-core pipeline version number
nf-core lint- Check pipelines code against nf-core guidelines

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Want more?

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snakemake workflows vs. nf-core
“nf-core is the more mature of the two projects”
“with a greater number of available pipelines”
“with a greater number of contributing authors”
“nf-core pipelines also benefit from a stricter and more extensively defined set
of guidelines for pipeline creation, testing, and synchronization”
“nf-core has a larger suite of helper tools for developers”

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https://gitter.im/nextflow-io/nextflow
And remember you can get help!!!
https://nf-co.re/join/slack

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nf-core/core

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www.bovregproject.eu
BovReg WP3 members
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 815668
Disclaimer: the sole responsibility of this presentation lies with the authors. The Research Executive Agency is not responsible for any use that may be made of the information contained therein.
LUKE
Johanna Vilkki
Dr. Daniel Fischer
GIGA institute-University of Liege
Carole Charlier
FMV-University of Lisbon
Luís Telo da Gama
Andreia J. Amaral
CRG
Paolo di Tommaso
Cedric Notredame
BovReg coordinator (FBN)
Christa Kühn
BovReg co-coordinator (INRA)
Dominique Rocha

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Thank you for your attention
www.bovregproject.eu
BovReg PARTNERS
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 815668
Disclaimer: the sole responsibility of this presentation lies with the authors. The Research Executive Agency is not responsible for any use that may be made of the information contained therein.

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Template synchronization