Companion project to NextflowWorkbench to help access Google Cloud storage in NW workflows and work interactively with data in the cloud.
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README.md

CloudInteractive

Overview

This software allows users to access, modify, and use their Google Cloud Storage files within MPS and NextflowWorkbench 1.6+

Usage

CloudInteractive provides several tools for Google Cloud Storage files.

CloudFolder retrieves cloud files stored at the given gs:// URL. Additionally, there is CloudInteractivePath, which will autocomplete your gs:// URL, given you have configured the Google Cloud Project ID via a CloudConfig node.

All of these tools have been integrated into NextflowWorkbench as input channels through the cloud.interactive.workflow language. Finally, there is a cloud file matcher input channel that takes a gs:// URL, and a regex or wildcard expression to match and fetch cloud files for usage within a workflow.

Credits

Access to Google Cloud Storage files provided by Google's API. CloudInteractive was developed by Radhika Mattoo to support cloud file usage/access within MPS and NextflowWorkbench.

Tutorial

See the following figures for examples of how to use the various tools within CloudInteractive via NextflowWorkbench:

Your first step should be configuring your Project ID via the CloudConfig node:

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For CloudFolder, create the folder and fetch your files. Then simply use autocomplete within the workflow to use it as an input channel.

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CloudInteractivePath is embedded in the NextflowWorkbench input channel editor as a Google Storage File Path Literal.

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The software will recognize if a string literal input is actually a gs:// URL, and will offer an intention to convert it for you.

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Use the file matcher input channel if you'd like to match multiple files within a cloud storage directory to a specific expression.

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You can use the inspector to cycle through the matched file names 5 at a time.

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