Feb 17, 2022 · Today, AWS for Genomics announces the addition of miniWDL as a workflow engine in Amazon Genomics CLI, an open source tool that makes it easier to run genomics workflows at-scale by automating the deployment of workflow engines and compute clusters.

Extends miniwdl to run workflows on AWS Batch and EFS. This miniwdl plugin enables it to execute WDL tasks as AWS Batch jobs. It uses EFS for work-in-progress file I/O, optionally uploading final workflow outputs to S3.

Nov 3, 2022 · WDL全称是 Workflow Description Language，是Broad Institute专门开发用来跑流程的语言。 WDL基本元件有5个，分别是定义总流程的workflow、定义单个任务的task、运行任务的call、定义任务中命令的command以及输出output。

Oct 13, 2021 · This post presents a new solution for deploying WDL workflows on AWS combining miniwdl with the Genomics Workflows Core (GWFCore). miniwdl is a lightweight WDL runtime, developed by the Chan Zuckerberg Initiative, focused on productivity for command-line interface (CLI) operators and workflow developers.

MiniWDL is a lightweight engine for running Workflow Definition Language (WDL) based workflows developed by […]

Feb 4, 2024 · This miniwdl plugin enables it to execute WDL tasks as AWS Batch jobs. It uses EFS for work-in-progress file I/O, optionally uploading final workflow outputs to S3.

The miniwdl runner schedules WDL tasks in parallel up to the CPUs & memory available on the local host; so a more-powerful host enables larger workloads. Separately-maintained projects can distribute tasks to cloud & HPC backends with a shared filesystem: AWS: miniwdl-omics-run tool for the Amazon Omics workflow service AWS Batch plugin (DIY) SLURM

Dec 13, 2022 · 集成了WDL、Nextflow、CWL 和 Snakemake等工作流语言，专为基因数据批量处理打造。 可以跟着 【伯乐大典】基于Nextflow基因组测序的AWS Batch实验（上） 一步步在workshop中练习。

This repository is a recipe for deploying miniwdl-aws and GWFCore to use within Amazon SageMaker Studio, a web IDE with a terminal and filesystem browser. You can use the terminal to operate miniwdl run against GWFCore's AWS Batch stack, the filesystem browser to manage the inputs and outputs on EFS, and the Jupyter notebooks to further analyze ...

Oct 12, 2020 · Miniwdl is a WDL interpreter and runtime (workflow runner). Like all foundational software, miniwdl started with a deep, informed focus on developer productivity: it emphasizes speed of execution, usable interfaces and abstractions, and good error messages that support the developer when something goes wrong.