19 papers · ranked by Valyu relevance
Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace, Francis Ouellette
'Francis Ouellette'] Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can…
Xinming Zhuo, Nicholas Renzette, Gregory Omerza
To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across various computational platforms through the implementation of…
Bishwa Ghimire, Nicholas Booth, Tapio Lönnberg, Tero Aittokallio + 1 more
Nextflow’s command-line interface has the optional flag -with-trace, which generates an execution tracing file trace.txt for a single pipeline run. Alternatively, Nextflow’s configuration file option (‘trace.enabled = true’) generates the execution tracing file for all pipeline runs as well. The file contains task…
Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber + 1 more
The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets…
Lukas Forer, Sebastian Schönherr
Nextflow has emerged as a flexible and scalable workflow system for building computational pipelines in life sciences. Simultaneously, Software-as-a-Service platforms enable researchers to concentrate on data analysis rather than on setting up pipelines locally. However, converting existing pipelines into web services…
Marek Sztuka, Krzysztof Kotlarz, Magda Mielczarek, Piotr Hajduk + 2 more
This study compared computational approaches to parallelisation of an SNP calling workflow. Data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome, post-alignment, and SNP calling. Three approaches to…
Marek Sztuka, Krzysztof Kotlarz, Magda Mielczarek, Piotr Hajduk + 2 more
'Jakub Liu' 'Joanna Szyda'] Title: Abstract This study compared computational approaches to parallelization of an SNP calling workflow. The data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome…
Fabrice Allain, Julien Roméjon, Philippe La Rosa, Frédéric Jarlier + 2 more
'Nicolas Servant' 'Philippe Hupé'] With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production…
Yash Patel, Chenghao Zhu, Takafumi N Yamaguchi, Yuan Zhe Bugh + 5 more
NFTest is a light-weight, customizable and easy-to-use method for automating testing of Nextflow workflows. With Nextflow offering a wide range of features such as multiple config files, configuration profiles, and parameter files, pipelines often become complex. NFTest includes support for these features in the…
Khairul Alam, Banani Roy
Scientific Workflow Systems (SWSs) such as Galaxy and Nextflow are essential for scalable, reproducible, and automated bioinformatics analyses. However, developing and understanding scientific workflows remains challenging for many domain scientists due to the complexity of tool/module selection, infrastructure…
Khairul Alam, Banani Roy
Scientific Workflow Management Systems (SWfMSs) such as Nextflow have become essential software frameworks for conducting reproducible, scalable, and portable computational analyses in dataintensive fields like genomics, transcriptomics, and proteomics. Building on Nextflow, the nf-core community curates standardized…
Huichao Zhang, Liao Qu, Yiheng Liu, Hang Chen + 32 more
Huichao Zhang\ 1 , Liao Qu\ 1 , Yiheng Liu\ 1 , Hang Chen\ 1 , Yangyang Song\ 1 , Yongsheng Dong\ 1 , Shikun Sun\ 1 , 2 , Xian Li\ 1 , Xu Wang 1 ,† , Yi Jiang 1 ,† , Hu Ye 1 , Bo Chen 1 , Yiming Gao 1 , Peng Liu 1 , Akide Liu 1 , 3 , Zhipeng Yang 1 , Qili Deng 1 , Linjie Xing 1 , Jiyang Liu 1 , Zhao Wang 1 , Yang Zhou…
Lukas Forer, Sebastian Schönherr
nf-test is implemented in Java as a command-line program, shares the same requirements as Nextflow, and is compatible with Linux and macOS. We adapted well-established testing concepts from software and web development for use in Nextflow pipeline testing. nf-test is built on a modular architecture and utilizes a…
Lukas Forer, Sebastian Schönherr
The workflow management system Nextflow builds together with the nf-core community an essential ecosystem in Bioinformatics. However, ensuring the correctness and reliability of large and complex pipelines is challenging, since a unified and automated unit-style testing framework specific to Nextflow is still missing.…
Kathleen West, Yehia Elkhatib, Lauritz Thamsen
Scientists in many fields, including genomics, materials science, and remote sensing, need to analyse increasing amounts of data [1, 4, 8, 9]. Scientific workflow systems facilitate the automation of such analyses, enabling scientists to compose pipelines out of black-box tasks with data dependencies between them. As…
Kathleen West, Youssef Moawad, Philipp Thamm, Vasilis Bountris + 4 more
As data-intensive scientific workflows scale to facilitate the automation of analysis of increasing amounts of data, their resource-intensive and long-running execution incurs significant energy consumption and carbon emissions. Given the already significant and rising emissions from the ICT sector, it is crucial to…
Authors not listed
The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely…
Luiza Nacshon, Rami Puzis, Polina Zilberman
OpenFlow is a protocol implementing Software Defined Networking, a new networking paradigm, which segregates packet forwarding and accounting (performed on switches) from the routing decisions and advanced protocols (executed on a central controller). This segregation increases agility and flexibility of a networking…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…