These are chat archives for nextflow-io/nextflow

12th
Jun 2017
Stian Soiland-Reyes
@stain
Jun 12 2017 10:13

@pditommaso could you double-check if my paragraph here is sane? (It's for a draft paper "Advances in technology for NGS")

Nextflow [https://doi.org/10.1038/nbt.3820] is a Python-like language for data-driven computational bioinformatics pipelines, with a strong focus on reproducibility and scalability. Nextflow uses Docker [https://www.docker.com/] for containerizing and deploying the third-party tools the workflow relies on. A Nextflow is declared by defining processes, which consume and produce messages on asynchronous channels. Channels are then wired together to form a workflow, which can be executed efficiently on a multitude of HPC and cloud platforms, including SGE, LSF, SLURM, Apache Ignite and Kubernetes.

anything important to add? E.g. any tools supported out of the box?
Paolo Di Tommaso
@pditommaso
Jun 12 2017 10:19
@stain I will you know in the afternoon, thanks!
Stian Soiland-Reyes
@stain
Jun 12 2017 10:27
Cheers!
Phil Ewels
@ewels
Jun 12 2017 11:42
"A Nextflow is declared" - is this a typo? Looks like it should be "A Nextflow workflow is declared" (not sure that "Nextflow" is a noun..?)
Paolo Di Tommaso
@pditommaso
Jun 12 2017 12:04
Yes, I would put A Nextflow pipeline is declared to avoid nextflow workflow that doesn't read so well
Stian Soiland-Reyes
@stain
Jun 12 2017 12:15
thanks
Paolo Di Tommaso
@pditommaso
Jun 12 2017 12:16
I would also add strong focus on reproducibility, portability and scalability
Stian Soiland-Reyes
@stain
Jun 12 2017 12:17
right, I had that before I moved out the Docker bit. Putting it back in!
Paolo Di Tommaso
@pditommaso
Jun 12 2017 12:17
Also I would mention the support for Singularity which is very important for HPC
Nextflow provides a built-in support for Docker and Singularity [https://doi.org/10.1371/journal.pone.0177459] container technologies which allows the packaging and the deployment of any third-party tool on which the workflow may rely on.
Stian Soiland-Reyes
@stain
Jun 12 2017 12:44
great, yes, that is important. Will have to add acknowledgement to you now :)
careful now so you don't become co-author!
or you will be guilty about promoting Snakemake
Paolo Di Tommaso
@pditommaso
Jun 12 2017 12:44
ahah, for so little ;)