Slides from my talk at a GenomeWeb webinar, I discuss how we use Nextflow at the SciLifeLab National Genomics Infrastructure and how this led to the founding of the nf-core community project.

1. Reproducible bioinformatics workflows
with Nextflow and nf-core
Phil Ewels
phil.ewels@scilifelab.se
https://scilifelab.se
https://ngisweden.scilifelab.se

2. 2020
62,789
samples
1112
projects
765.3
x1012 base pairs
Human genome
every 2 minutes
1X

3. https://www.nextflow.io/

4. https://www.nextflow.io/
SGE
PBS
LSF
Singularity

5. A community effort to collect a
curated set of analysis pipelines
built using Nextflow.
https://nf-co.re

6. Guidelines Tools Pipelines
https://nf-co.re

7. Develop with
the community
Start from the
template
Collaborate,
don’t duplicate
https://nf-co.re

8. 33
RELEASED
15
UNDER DEVELOPMENT
5
ARCHIVED
https://nf-co.re

10. https://nf-co.re/stats

11. https://nf-co.re/community

12. https://nf-co.re/join

13. Requirements
1
2 or or
3
/tools

14. Running a pipeline
nextflow run nf-core/<pipeline> -r <version>
GitHub pipeline name
Clones to ~/.nextflow
Pipeline release tag
Repository branch

15. Running a pipeline
nextflow run nf-core/<pipeline> -r <version>
--input my_samples.csv --genome GRCh38
Parsed as params.genome = 'GRCh38'
Can be supplied in a file (config / YAML / JSON)

16. Running a pipeline
nextflow run nf-core/<pipeline> -r <version>
--input my_samples.csv --genome GRCh38
-profile docker
Specifies a configuration profile
Common setups bundled with pipelines, also
shared institutional profiles available

17. Running a pipeline https://nf-co.re/rnaseq

18. Running a pipeline https://nf-co.re/launch

19. Running a pipeline
nf-core launch --id 1637063024_d92e0f1632c2
nextflow run nf-core/rnaseq -params-file nf-params.json
https://nf-co.re/launch

20. Running in the cloud

21. Running in the cloud https://github.com/nf-core/viralrecon

22. Running in the cloud https://nf-co.re/viralrecon

23. Running in the cloud https://nf-co.re/viralrecon

24. Phil Ewels
Photos: Mattias Ormestad, unsplash.com
@ewels
@tallphil
Ewels, P.A., Peltzer, A., et al.
Nat Biotechnol 38, 276–278 (2020).
https://doi.org/10.1038/s41587-020-0439-x
https://www.nextflow.io
https://tower.nf
https://phil.ewels.co.uk
phil.ewels@scilifelab.se
https://nf-co.re
https://ngisweden.se
https://scilifelab.se
https://multiqc.info
https://megaqc.info
https://sra-explorer.info/