NextFlow specifications

Information


Unique identifier OMICS_25663
Name NextFlow
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Groovy, Java, Javascript, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.27.0-RC2
Stability Stable
High performance computing Yes
Maintained Yes

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Documentation


Maintainers


  • person_outline Cédric Notredame <>
  • person_outline NextFlow Team <>

Additional information


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

Publication for NextFlow

NextFlow in publications

 (12)
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] identified using the maker recommended method (). to ensure comparability of results between assemblies and reproducibility of results more generally, the method was formalized as a reproducible nextflow pipeline (). the pipeline is available at http://doi.org/10.5281/zenodo.1098651., long terminal repeat (ltr) elements were detected using two parallel runs of the ltr harvest () […]

PMCID: 5895046
PMID: 29601575
DOI: 10.1371/journal.pntd.0006368

[…] raw and tpm (transcripts per million) read counts for annotated genes, respectively. deseq2 [] was used to identify differentially expressed genes. the complete rna-seq pipeline was implemented with nextflow [] and is publicly available through github (www.github.com/andersenlab/bzrna-seq-nf)., we examined natural variation in c. elegans responses to four benzimidazoles (albendazole, […]

PMCID: 5850084
PMID: 29568489
DOI: 10.5256/f1000research.14771.r31487

[…] being hosted on a different host environment. once encapsulated this way, analysis pipelines were shown to become entirely repeatable across platforms., several workflow management systems, such as nextflow, toll and galaxy, have recently been reported as having the capacity to use and deploy containers. these tools all share the same philosophy: they make it relatively easy to define […]

PMCID: 5691353
PMID: 29048555
DOI: 10.1093/gigascience/gix099

[…] have emerged, allowing the user to combine analytical tools and build pipelines using graphical interfaces. in addition, workflow management systems (such as taverna [], galaxy [], snakemake [], nextflow []) also ensure the traceability and reproducibility of the analytical process. the efficient use of a workflow management system remains limited to trained bioinformaticians., docker […]

PMCID: 5508203
PMID: 28695896
DOI: 10.1038/ncomms15945

[…] to convert mouse gene symbols to human gene symbols. we used deseq2 to perform all differential expression analyses (v1.12.3), and utilized nextflow (http://dx.doi.org/10.6084/m9.figshare.1254958) to implement our computational pipelines., cas9-induced mutations were detected using the t7 endonuclease i (neb). briefly, an ∼500 bp region […]


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NextFlow institution(s)
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
NextFlow funding source(s)
Supported by the Center for Genomic Regulation and the Spanish Plan Nacional and the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, La Caixa Foundation, and the CERCA Programme/Generalitat de Catalunya.

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