Scalable, reproducible bioinformatics workflows using Nextflow & nf-core
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/6316389/nextflow_logo.png)
Alexander Peltzer
ELIXIR Workshop on FAIR Computational Workflows
September 2, 2020
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
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Dataflow Model
Domain-specific language
Executor abstraction
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![](https://upload.wikimedia.org/wikipedia/commons/thumb/3/3a/Slurm_logo.svg/1200px-Slurm_logo.svg.png)
![](https://developer.nvidia.com/sites/default/files/akamai/cuda/images/product_logos/Univa_red_box_340x190.jpg)
![](https://www.aspsys.com/images/solutions/software-solutions/hpc-schedulers/pbs-works-logo.png)
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![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
Tools
Guidelines
Pipelines
A community effort to collect a curated set of analysis pipelines built using Nextflow.
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
- 25 stable
- 15 in development
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7688400/Bildschirmfoto_2020-09-02_um_10.36.56.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
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Github Actions: CI Testing
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![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
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 │
╰───────────────────────╯
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
JSON Schema
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7686956/Bildschirmfoto_2020-09-01_um_22.03.54.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
JSON Schema
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7686955/Bildschirmfoto_2020-09-01_um_22.07.50.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
JSON Schema
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7687088/Bildschirmfoto_2020-09-01_um_22.47.34.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
Nextflow Tower
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7686964/Bildschirmfoto_2020-09-01_um_22.13.13.png)
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
AWS Megatests
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/7688412/Bildschirmfoto_2020-09-02_um_10.38.36.png)
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![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
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![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
FAIRification of nf-core
![](https://gui.dockstore.org/2.6.1-f71d7c6/assets/images/dockstore/logo.png)
Dockstore (supported)
ro-crate (prototyping)
Evaluating
JSON Schema
![](https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nf-core-logo.png)
![](https://s3.amazonaws.com/media-p.slid.es/uploads/731815/images/6316389/nextflow_logo.png)
ECCB2020 NXF + NF-Core
By Alexander Peltzer
ECCB2020 NXF + NF-Core
- 2,884