Nextflow

Service to run Nextflow pipelines

The command line service provides the necessary environment to run any Nextflow pipeline. The basic command for using the service after logging in is: nextflow run <pipeline_name> For a collection of curated containerised pipelines used by biological core facilities see nf-core (http://nf-co.re).

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For developers

Type:

Software, Service, Workflow tool

Categories:

Processing and analysis

Applicability domain:

Bioinformatics

Targeted industry:

Drugs, Chemicals, Nanotechnology

Targeted users:

Software Developers, Researchers, Students

Relevant OpenRiskNet case study:

TGX - Toxicogenomics-based prediction and mechanism identification

Support service:

https://www.seqera.io/

Support contact:

Paolo Di Tommaso info@seqera.io

Documentation:

https://www.nextflow.io/docs/latest/index.html

References and training materials:

GitHub: https://github.com/nextflow-io/nextflow

Gitter Support Channel: https://gitter.im/nextflow-io/nextflow/

Google Forum: https://groups.google.com/forum/#!forum/nextflow

Publication: https://doi.org/10.1038/nbt.3820

If you use Nextflow in your research, please cite:

P. Di Tommaso, et al. Nextflow enables reproducible computational workflows.

Nature Biotechnology 35, 316–319 (2017) doi:10.1038/nbt.3820

Provided by:

Centre for Genomic Regulation (CRG)

Contact:

evan.floden@crg.eu @evanfloden

Licence:

Apache 2.0

Login required:

Yes

Implementation status:

Containerised

Integration status:

Integration in progress

Service integration operations completed:

Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.

Is annotated according to the semantic interoperability layer concept using defined ontologies.

Is containerised for easy deployment in virtual environments of OpenRiskNet instances.

Has documented scientific and technical background.

Is deployed into the OpenRiskNet reference environment.

Is listed in the OpenRiskNet discovery services.

Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).

Provides legal and ethical statements on how the service can be used.