ArticleGigaScience2019
CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- An open-source platform for structured annotation and computational workflows in digital pathology research.Scientific reports · 2025Article
- Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach.bioRxiv : the preprint server for biology · 2024Article
- KMT2D regulates activation, localization, and integrin expression by T-cells.Frontiers in immunology · 2024Article
- TSLP shapes the pathogenic responses of memory CD4Science signaling · 2023Article
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- Framing Apache Spark in life sciences.Heliyon · 2023Review
- Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).Frontiers in bioinformatics · 2023Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- CONTROL-CORE: A Framework for Simulation and Design of Closed-Loop Peripheral Neuromodulation Control Systems.IEEE access : practical innovations, open solutions · 2022Article
- Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.STAR protocols · 2021Article
- Design considerations for workflow management systems use in production genomics research and the clinic.Scientific reports · 2021Article
- Article
- Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics.Biology · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- Impact of concurrency on the performance of a whole exome sequencing pipeline.BMC bioinformatics · 2021Article
- Article
- PM4NGS, a project management framework for next-generation sequencing data analysis.GigaScience · 2021Article
- Software-Defined Workflows for Distributed Interoperable Closed-Loop Neuromodulation Control Systems.IEEE access : practical innovations, open solutions · 2021Article
- Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets.GigaScience · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundMassive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL.
findingsHerein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided.
conclusionsCWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run-from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.