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Release Notes

These release notes intend to document the changes to Cirro most relevant to our user base and therefore this list is not exhaustive. Please contact the Cirro team with any questions.

June 2025

Bug fixes

  • Fixed an issue where shared datasets did not work with paths pulled from sample sheet.
  • Fixed an issue where Project admins were getting a permissions error while managing notebook instances.
  • Fixed intermittent "signature invalid" message during file upload.

New features and improvements

  • Basic Compliance reporting: Organization and project administrators can now easily view when users have configured and completed governance requirements using the "Governance Summary" buttons while editing projects and users in their respective pages.
  • Nextflow based pipelines automatically use a project level task cache. Users no longer have to specify a previous pipeline run via the "Copy parameters from" field.
  • When setting governance requirements for projects, organization administrators are now able to require that project administrators provide the agreement or document file to meet the needs of their specific project.
  • Individual files can now be selected from the samples table when running a pipeline.
  • AWS Batch compute environment deployment adapts to regional availability of instance types.
  • Nextflow executor for pipelines upgraded to 25.04.2.
  • UI refinements.

May 2025

  • Project administrators can now set agreement, document, and training governance requirements for their project and require compliance by users before accessing the project. Admins can set these requirements in the governance section of the project's Overview page.
  • When uploading a samplesheet after creating a dataset, you can now upload either .xlsx or .csv and use any file name. After upload, the file will be automatically re-named to samplesheet.csv in uploaded dataset.
  • Solved an issue where pipeline runs would not be cleaned up properly after terminating an analysis.
  • Fixed a bug with rendering mermaid diagrams in inline pipeline documentation.

April 2025

  • You can now select a subset of samples to include when running a pipeline. Custom pipelines can be set up to support this feature in their configuration through the "Pipeline supports Cirro sample sheet" option.
  • The Cirro Pipeline Configurator tool is now available for use. This tool allows users to create and manage pipeline configurations for integrating with the Cirro platform.
  • Add a new user role of "system administrator," who have all the same permissions as "tenant administrators," except for restricted access when viewing and downloading project data from projects where they are not an added member. Due of the significant overlap in permissions between system administrator and tenant administrator, our documentation will refer to both roles as "organization administrator", unless there is a case where their permissions differ.
  • Fixed a bug with extracting sample information from certain file name formats.

March 2025

  • We have released the first iteration of our Governance Feature Set which allows organization administrators to assign and track policy compliance of projects across their organizational tenant. Organization admins can now upload documents, assign agreements and trainings to project users, and require completion before allowing access to project data in order to ensure compliance.
  • Dataset sharing is now available in Cirro. Project administrators can share groups of datasets with other projects, and can accept incoming shares. Datasets from shares will appear on the Datasets page like normal, flagged with a new share icon, and can be used in running analysis pipelines with no changes to your normal workflow. Learn more about Dataset Sharing and visit the new Shares page in your projects.
  • Added a new Account Settings page where users can edit their profile and notification settings.
  • Fixed a bug when calculating the total project storage on the project's Costs page.
  • New Pipelines: Decontaminate Metagenome (KneadData)

February 2025

  • Added new options for projects so administrators can configure the retention of temporary storage (used for things like the workflow executor cache) and a max-CPU option for Field-Programmable Gate Array (FPGA) instances.
  • Fixed bug where Cromwell reports didn't generate when workflows failed.
  • Tenant administrators can now view and filter billing reports directly in Cirro without having to download them. They also have the option to download reports as either Excel spreadsheets or CSV files.
  • We now allow certain users to flag custom pipelines as available to all projects in their organization.
  • Added an option to the sarek pipeline to run Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient.

January 2025

  • Improved usability of the execution logs viewer on the dataset Overview page by adding adjustable columns, full-screen options, and easy access status icons.
  • When adding your own custom Nextflow and Cromwell pipelines to Cirro, you can now define the expected file outputs from the pipeline, including specifying the number of files and multiple file matching patterns for each expected file type.
  • Fixed an issue in project requests so now project administrative contacts do not have to be existing Cirro users.
  • New Pipelines: nf-core fastquorum, Nanopore Variant Calling

December 2024

  • We've added a new help menu in Cirro's header which can be used to easily access the documentation website, the status website, the Cirro support email, and any internal emails for organization-specific questions.
  • You can now view the actual start time of a process, separate from the time the process was requested, in the execution logs on the dataset's Overview page.
  • Organization administrators can now set up compute environments for individual projects by opening the project's settings and choosing the "Compute Environments" button.
  • Users can now manually select a subset of files from a dataset to download.
  • New Pipelines: Quantitative Spatial Analysis

November 2024

  • To help streamline the process of adding a new project, Cirro now has a "Request a New Project" button at the top of the Projects page available for certain users. It will ask you for some details on your potential project and send your information to the appropriate team to fulfill your request.
  • Organization-wide administrators will now have access to the new System section of Cirro. In this section, they will be able visit pages where they can to view all their tenant's projects, manage users across their organization, define data classifications for projects, and more.
  • We now offer support for users to run their workflows on local compute resources. Organization administrators can set up access to these resources on the Agents page.
  • Fixed an issue where Nextflow pipelines were not being automatically retried on Spot instance termination.
  • New Pipelines: Cellpose Cell Segmentation

October 2024

September 2024

  • You can now view your high-resolution multiplexed bioimaging data directly on your dataset's Overview page.
  • The Pipelines page has been updated to provide more filtering options including pipeline category (e.g. DNA Sequencing, Proteomics, etc) and pipeline type (e.g nf-core, Ready2Run, etc).
  • Introduced a new feature to help users easily authorize access to their private GitHub repositories within Cirro.
  • New Pipelines: INDELpred

August 2024

  • Now you can directly request access to a project rather than having to contact the Cirro team. Users can use the "Request Project Access" button on the Projects page to send an automated email the project admins. Learn more about requesting access to projects and how project admins can approve or deny requests.
  • Fixed a bug where commit hash displayed on the info pop up for custom pipelines wasn't updated correctly after syncing.
  • Fixed a bug on multiple pages where the search fields would return results based on where the search parameter was in the string.
  • We have replaced the use of Cirro usernames and passwords with emailed magic links. If you previously used a Cirro password to log in, you will now be emailed a link that you can click which will automatically log you in and re-direct you to the website. This only applies to Cirro-specific passwords; if you are logging in through your organization, you may still need to use that password.
  • Fixed an error in various CLI/SDK commands so users can provide project or dataset names instead of IDs.
  • New Pipelines: Flow Cytometry - Analyze Control Beads

July 2024

June 2024

  • Users creating custom ingest pipelines can now specify their own sample matcing regex patterns so as to pull sample information from known file names. Learn more about adding regex patterns to file types.
  • We've expanded current permissions so the owners of custom pipelines can flag which projects are allowed to use their pipeline. This option if available when the user imports their pipeline into Cirro.
  • You can now easily inform people that you have added them to your project by clicking the new "Send notification to user" button in the Add User pop up. This will send new users an email with details on the new project.
  • New Pipelines: nf-core/differentialabundance

May 2024

  • Extra large datasets (>35,000 files) are now supported by Cirro.
  • You can now bring your own AWS account to Cirro with our new, self-service process. Please contact the Cirro team if you are interested in using this feature.
  • Cirro now supports multiple organizations. On the cirro.bio homepage, you will now need to select your institution or the "Independent Researcher" category. You can now update your bookmarks for your institution-specific Cirro link.
  • New Pipelines: proseg, nf-core/mag