Nextflow Sandbox (version 2) Extension for Visual Studio Code

This extension provides convenient tree views and ease-of-use utilities for managing, configuring, running, and debugging Nextflow pipelines.

Features

• Quickly create new pipelines which reference existing Nextflow repositories, scripts, configurations, and parameter files

• Specify the storage folder location for the work folders and files created by Nextflow runs

• Set options and arguments for the Nextflow command-line

• Execute Nextflow Run, Resume, Config, and Pull with one click (versus typing the command into a terminal)

• Automatically group and decorate work folders using human-readable process names instead of cryptic hexidecimal process identifiers

• Open work folders in a terminal or reveal them in the finder with one click

• Launch Docker container with process work folder mapped with one click (for processes utilizing Docker)

Requirements

Nextflow

Extension Settings

This extension contributes the following settings:

• nextflow-sandbox.executablePath: path to the Nextflow executable
• nextflow-sandbox.storagePath: path where Nextflow will store local work
• nextflow-sandbox.autoShowLog: automatically show log upon Nextflow exit
• nextflow-sandbox.shellPath: custom shell executable path
• nextflow-sandbox.shellArgs: custom shell executable args

Known Issues

None

Release Notes

I created this extension for my personal use, as my daily activities generally include running one or more Nextflow pipelines, and I wanted to automate the features that I exercise most.

As an isolated user, the use-cases I have added support for are clearly limited to my personal experience using Nextflow. If you find this extension useful, I am very interested in receiving feedback, including any issues encountered with its use, as well as features not implemented that would be useful to you. I am happy to update this extension so that everyone may benefit.

If you would like to report a bug or feature request, please do so on the github repository for this project. I will make every effort to respond in a timely manner.

If you enjoy using this extension, please leave a rating!

0.0.1

Initial release of Nextflow Sandbox.

0.0.2

Removed unnecessary quotes around the '--args' parameter.

0.0.3

Added optional selection of the pipeline storage path when creating a new pipeline.

0.0.4

Fixed issue caused by singular args value.

0.0.5

Added port mapping to Launch Container when launching docker container, to support java remote debugging.

0.0.6

Removed "stopped" description on pipelines; now only displays "running" when running.

0.0.7

Added support for project repositories.

0.0.8

Added "pull" Nextflow command support.

0.0.9

Added extension icon.

0.1.0

Added support for launching a container with 1+ spaces within the pipeline path.

0.1.1

Fixed issue caused by multiple spaces within the pipeline path when launching a container.

0.1.2

Found an issue with escaped characters in the Nextflow container run command when launching a container from a pipeline with spaces in its name; opted to replace spaces with underscores when creating a pipeline to bypass the issue altogether; may revisit at a later date.

0.1.3

Now handles escaped characters in the Nextflow container run command when launching a container from a pipeline with spaces in its name.

0.1.4

Resolved an issue caused by incorrect placement of the configuration file option (-c) when executing the Nextflow config command.

Removed automatic port mapping with Launch Container when launching docker container, as it would fail if the port was already in use.

0.1.5

Resolved issue with command args.

Removed "profile" configuration setting, as this may be set in the "args" configuration setting, and was therefore redundant.

0.1.6

Removed "Resume" context menu item for pipelines, as this may be set in the "args" configuration settings (-resume), and was therefore redundant.

0.1.7

Removed notion of archiving previous runs, as this prevents resuming.

0.1.8

Added "Configure from nextflow run command-line..." pipeline context menu item, which parses a nextflow run command-line and formulates the pipeline configuration from that.

0.1.9

Updated "Configure from nextflow run command-line..." to better handle arbitrary project repo/script placement within the command-line.

0.2.0

Added shellPath and shellArgs settings.