a.k.a. The Swedish Childhood Tumor Biobank
Collect pediatric solid tumors samples (+ blood)
6 Swedish University Hospitals
Store samples
National research resource
Pediatric cancer samples and genomic data
Share samples
Analyse and share data
a.k.a. National Genomics Infrastructure
State-of-the-art infrastructure
Guidelines and support
Sample collection, study design, protocol selection
Bioinformatics analysis
Workflow manager
Data driven language
Portable
executable on multiple platforms
Shareable and reproducible
with containers or virtual environments
NGI had been developing analysis pipelines for years and using a set of standards
This helped other group run the pipelines on their own
Pipelines began to outgrow the SciLifeLab/NGI
branding
In late 2017, nf-core
was created, thanks to Phil Ewels ( NGI ), Alex Peltzer ( QBiC ), Sven Fillinger ( QBiC ) and Andreas Wilm ( A*STAR )
All relevant pipelines were moved to this new GitHub organisation
What we want in our pipelines
Nextflow based
Common structure (based on our nf-core template)
Stable release tags
MIT license (can be used even in commercial settings)
Using biocontainers (if possible)
Continuous Integration testing ( GitHub Actions )
One pipeline per data type/usage ( lagom )
Our website has pages for each pipeline that renders the documentation available on GitHub
33 released pipelines
27 in development
Configurations
All pipelines come with a default sensible configuration for a regular sized HPC
nf-core/configs allows shared configurations between pipelines for a specific HPC
cpus, time and memory requirements
scheduler
queues
environments
path to common references files
Modules are the building stones of all DSL2 nf-core blocks.
Can be used outside nf-core as well.
Demo
curl -s https://get.nextflow.io | bash
nextflow run nf-core/sarek -r dev -profile test ,docker
Acknowledgements
Resume presentation
What is nf-core? Maxime U Garcia ▸ @gau | @maxulysse Karolinska Institutet | Science for Life Laboratory Sweden
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