1.6.2 November 2 2016

  • Upgraded to MPS 3.4.0.

1.6.1 August 29 2016

  • New concepts that abstract/manipulate access to the memory assigned to the process instance.
  • Introduce a new type of function closure that allows to use plain text code in the closure’s block. The code in the block is generated “untouched” in the workflow’s output.
  • Upgrade the nextflow installer packaged with the workbench to version 0.21.2.
  • Hyperlink process execution traces to working directory (either local or remote) of the process instance. This makes it easier to follow the execution of workflows. Developed by Radhika Matoo.

1.6.0 August 9 2016

  • Upgraded to MPS 3.3.5.
  • Support for docker native (tested on Mac, please let us know if you have issues on Windows).
  • Fixed type of splitCSV when no headers are provided.
  • Interactive support for Google Cloud Storage in companion project CloudInteractive.
  • Allow to specify the version of nextflow to run, including snapshot versions.
  • Support to increase memory each time a process execution fails.

1.5.5 Jun 28 2016

  • Bundle nextflow in the Nextflow-Workbench plugin. No need to manually install it and configure NEXTFLOW_PATH variable anymore.

1.5.4 Jun 27 2016

  • Use the new elasticluster-config-tools image to provision the cloud cluster.
  • Cloud cluster: check that docker is able to connect to the network, restart it as needed.
  • Cloud cluster: reconfigure compute nodes in the GE queue according to their available memory.
  • Reorganize models and processes in rna-seq based according to the tool(s) used in each process.
  • Allow to enable/disable the remote configuration in the workflow.config.
  • Add possibility to set docker run options in workflow.config
  • New function constantRepeat for input channels.
  • Add memory dynamic option when retrying a failed process (this requires recent version of nextflow, use nextflow self-update as needed).

1.5.3 May 23 2016

  • Install the software on each cluster node with ansible (parallel installations).
  • Reconfigure the Grid Engine queue to execute multiple jobs on each node in the cluster according to its physical cores.
  • Adjust the font on the icon displayed for several concepts (see https://youtrack.jetbrains.com/issue/MPS-23772).

1.5.2 Apr 14 2016

  • Grant access to the cluster with gcloud SDK
  • Validate cluster name according to gcloud SDK specifications.
  • Minor fix on constant value’s duplication in the workflow.
  • Allow to optionally load the environment before the script execution in a Process. By default, it is enabled.
  • Automatically mount the scratch folder when running inside a docker container and executing with SGE.
  • Add gsutil to artifacts/software image. gsutil can be used to pull and push data to/from Google Cloud Storage within a process.

1.5.1 Apr 6 2016

  • Extend cloud configuration language to set cluster name, zone and shared NFS size.
  • Install java 8 instead of java 7 on each cluster node.
  • Allow input constant values to be duplicated in the workflow.
  • Remove checks on the local software installation when submitting to the cloud or a remote cluster.
  • Bind the cluster manager to a specific tag of the docker image used to create the cluster.
  • Fix execution of the workflow’s report section on the cloud.

1.5.0 March 28 2016

  • Added cloud configuration language to provision a cluster with Google Cloud Platform.
  • Updated documentation to describe new cloud capabilities. See Section 7.5 of the documentation booklet.

1.4.2 Feb 9 2016

  • Simplified Docker and Workflow configurations. Many required options are now automatically detected and set..
  • Intentions to duplicate Global and Output Channels create 2 channels by default. More can be added by the user as needed.
  • Check that single quotes match around file pattern a channel declaration.
  • Report an error when a process name has spaces (not allowed).
  • Rename processes in the Samples.training model to avoid confusion with processes included in the rna-seq solution.

1.4.1 Jan 28 2016

  • See updated Installation Instructions.
  • New intentions to duplicate Global and Output Channels to be reused as input by different processes.
  • Added solution rna-seq to the plugin.
  • Allow to run docker-based processes imported from other models.
  • New consistency checks among process and docker/workflow configuration.
  • Added capability to run an R script as process.

1.4.0 Jan 15 2016

  • NextflowWorkbench was upgraded to MPS 3.3.

1.3.1 Nov 4 2015

  • Added intention to create a frozen image for a GobyWeb script with resources defined in a BASH script or nextflow Process.
  • Fix icons when running from the plugin
  • Add HiDPI version of icons for better looking icons on retina displays.

1.3 Oct 29 2015

  • Frozen production environment for clinical applications or fully reproducible runs for publication. Install GobyWeb resources inside the image, so that a container can start immediately with installed resources. Provide easy switch from development to production environment.
  • Improved auto-completion for artifact paths and paths inside the docker image(for instance, auto-completion will now warn you if the interactive container is not running).
  • Provide the ability to specify a current directory for interactive containers, so that relative path auto-completion knows what suggestions to offer when auto-completion is invoked.
  • Add Salmon 0.5.0 to the list of resources that can be installed as a GobyWeb resource.

1.2 Oct 8 2015

  • New features to use the workbench as a Docker IDE. Edit Dockerfiles, build images, tag, push, pull, and run images interactively.
  • Develop Bash scripts and Nextflow processes for execution inside a docker container
  • Auto-install GobyWeb resources (for tens of popular bioinformatics tools) including software, but also data and indices.

1.1 September 2 1015

  • Add support for most functions offered by Nextflow.io
  • Add support for closures
  • Implement constants (e.g., variables that do not create channels, but whose value is always the same and can be used directly inside a nextflow.io process).
  • Implement command line parameters, a variation on constants, where initializer is taken from values on the command line. 
  • Add ability to specify command line parameter in the run configuration.
  • Support resuming a workflow (see new “resume” option in run configuration)
  • Documentation was updated with a new Chapter describing how to use functions, and differences with Nextflow.

1.0.2 August 27 2015

  • Add debug statements to help troubleshoot problems with workflow execution.
  • Fix workflow execution issue on Linux and Windows (GitHub issue #3).

1.0.1 August 19 2015

  • Documentation: added Execution and Configuration Chapters.
  • Documentation: added a Getting started video tutorial on the project page (https://www.youtube.com/watch?v=6jMdOomiFx8).
  • Fixed major problem with run configuration that prevented running workflows reliably. Ability to run workflows was lost after closing the project.
  • Fixed bug that prevented generating a workflow when not in the model. For instance, generating sample workflows from the plugin would required copying the workflow to a model in a project.
  • Removed dependencies on NYoSh, logger and UI plugins. This dependency caused an additional path variable to be reported as missing upon first startup, and made installation a two step process (logger was missing in the dependencies section and MPS 3.2.3 apparently does not calculate the full list of dependencies from the ones declared).
  • Report an error if remote submission is selected for execution, but there is no remote submission section in the configuration node.

1.0 August 7 2015

Initial release of the Nextflow workbench.