Seqera Platform Feature Requests

This project will introduce versioning capabilities to Seqera Platform, allowing users to create, save, and reference different versions of pipelines based on their configuration and parameters. Planned Features Automatic Version Tracking Automatic version creation whenever a pipeline is created, modified, or launched with edited restricted parameters Checksum-based tracking for pipeline integrity and provenance Version Management Users with pipeline edit capabilities can assign custom labels to pipeline versions Ability to set any version as the default for launch Option to save completed workflow runs as new versions Restricted Parameter Control Users with pipeline edit capabilities can modify restricted parameters at the pipeline level Locked configurations for users with launch-only permissions to ensure controlled pipeline execution Support for custom nextflow_schema.json files to define editable parameters Version Selection at Launch Default version shown in launch form for all users Users with pipeline edit capabilities can select and launch any version Launch-only users can select from available labelled versions Commit ID Tracking Store commit IDs alongside revision information for deterministic pipeline execution Option to pin to specific commits or use latest branch updates Target Users This functionality is intended for bioinformaticians who customise platform pipelines for themselves or their users, applicable to all customers including Enterprise requiring pipeline execution control.

Currently we have no way to integrate with GitHub Apps to allow for checking out of GitHub repositories. This means we need to use a full fledged GitHub account with a personal-access-token which can be a security risk as the account would only be used for Seqera Tower. This also makes us burn an organization wide account seat because of this limitation. We do not want to tie this access to a single user as we then have to update the GitHub access token after the person leaves. Please add support for GitHub Apps to checkout repositories instead of a full GitHub account + personal-access-token.

I am trying to record, track, and modify the state of my Seqera Platform instance. Its proven to be extremely difficult to adequately write out descriptions of all the settings and configurations I end up using in a simple README.md file. I have started resorting instead to the export and update functions of the CLI, such as: tw compute-envs export --workspace 1234567890 --id AbcAbcAbc > My_dev_CE_AbcAbcAbc.json tw participants list tw participants update ... tw workspaces list tw workspaces update ... tw pipelines list tw pipelines update ... While the CLI tool is invaluable for the ability to do all this Seqera Platform management from the cli, and in a potentially scripted manner, ultimately what I actually need is the ability to export all of the "configurable" components of Seqera Platform to a file, update that file as needed, and then upload it back to Seqera Platform to apply the changes. Essentially I think what I need is "Terraform for Seqera Platform", or something to that effect. Some way to not just manipulate individual aspects of the Platform but to also snapshot all of its configurations to a file that can be tracked in version-control, manipulated outside of Platform, and then used to apply the needed configuration changes to Platform. This would also have the benefit of allowing you to see the entire state of the Platform at once, instead of having to pull out single attributes one at a time. At a bare minimum, some sort of export all + import all in a YAML or JSON would help. Let me know what you think, thanks.

Currently, AWS Batch without Fargate and AWS Cloud CE are the only supported compute environments (CE) for Studios. Adding support for HPC environments (like Slurm) would benefit many customers who want to adopt interactive analyses within their HPC deployments.

It can be tough to quickly tell what page you are on when using Seqera Platform. Having headers displaying your place in the page map could assist. It would be great if it were easier to contextualize where you were in Seqera Platform at a glance and if there were a clearer hierarchy of menus. Also, breadcrumb navigation would be beneficial: Organization > Workspace > Participants Organization > Members Admin > Users With some colored highlighting, it might help to keep from getting lost in the menus and pages.

Datasets within Seqera Platform facilitate structured handling of input sample sheets required for genomics pipelines such as RNA-seq. Currently, researchers often face friction in assembling these datasets, needing to prepare CSV files externally. This could be improved by the following: 1. Remove/Increase Dataset limit: Users are currently limited to 1000 datasets per workspace. Action: Raise or remove limit 2. Improved Dataset listing: Currently, the dataset listing is relatively basic and low density. Around 6 datasets can be viewed in a typical desktop browser window size. This density plus lack of tooling hinders users from effectively navigating or identifying datasets quickly. Action: A metadata-rich table view, such as those used on the Runs page and elsewhere would be preferable. Such a table could include the dataset name, number of rows, author, creation date, last used date, and potentially the start of the description. The table will be sortable. 2. Dataset creation from Pipeline Launch UI: Currently, creating datasets requires users to navigate away from the pipeline launch page, disrupting workflow and causing friction. Action: Integrate dataset creation directly within the pipeline launch interface, users can seamlessly upload or enter sample data without leaving their primary task. 3. Enhanced Dataset details user interface: Currently, viewing dataset details emphasizes metadata over actual dataset content, causing users unnecessary scrolling and inefficiency. Action: Prioritizing the dataset’s actual content prominently at the top ensures users quickly verify the dataset's accuracy and completeness, reducing errors and improving productivity. 4. "Archive" or "deactivate" a Dataset: Datasets are often used once or twice, and then no longer actively needed. For GxP/clinical environments, the dataset should not be deleted/removed, but made inactive/disabled/"archived"/"deactivated". This allows inspection of the dataset, but it would be excluded from any pipeline launches. The table of datasets can be filtered to remove inactive/disabled/"archived"/"deactivated" entries. Action: Allow datasets to be tagged as “inactive/disabled/archived/deactivated” and allow filtering of datasets to show/hide archived entries. 5. Import or link a Dataset from a URL: Datasets are becoming increasingly available via URL links. Currently, users are forced to fetch locally and add them, adding friction and wasting storage, and the original reference of the source is lost. Action: Supporting direct URL import/linking. 6. Keep a record of Dataset usage in Runs: Currently, it’s difficult / impossible to know if a dataset has ever been used. This makes their utility post-usage very limited. Action: With a record of Dataset usage within Run history, Datasets suddenly become a powerful tool for the user. They act as a rich history of run inputs, agnostic to the specifics of pipeline design and file usage. 7. Improve how Dataset versioning works: A user should be able to choose any dataset and version as the source of a pipeline run, and that dataset and version is displayed in the pipeline Run details page in the “Datasets” tab correctly. Additional potential milestones Integration with new Nextflow data lineage

Our primary use case for the Seqera Platform involves one user setting up a workspace with preconfigured pipelines, accessible to others in the organization. We aim to preconfigure pipelines to a large extent, yet allowing for minor, user-specific or pipeline-specific customizations. If variables could be included in paths, which are evaluated at pipeline launch, a tidier directory structure accommodating many different users and pipelines would be possible. Therefore, I propose that a distinct set of variables should be supported by Seqera Platform/Tower: username , pipelinename , pipelinerevision , workspacename and date come to my mind. All are "known" to the Platform when launching a pipeline, but may not exist yet. Therefore, the respective paths must be created automatically by the agent, if not available on the HPC / cloud provider. For instance, a work directory could be preconfigured as: /path/to/a/work/directory/{{username}}/{{pipelinename}}/{{runname}} Parameter files could be specific to a pipeline revision: /path/to/a/params/{{pipelinename}}/params-{{pipelinerevision}}.json and account for changing parameters. This would streamline the management of configurations, parameters, work directories, launch directories, and outputs across numerous users and pipeline runs.

Update the current user role permissions to manage more fine-grained permissions (Role Based Access Control, etc).

It would be great to have a feature built directly in to the Seqera Platform that allows users to generate a support ticket with all logs attached automatically or even just a feature in the platform that a user could click to gather all relevant support logs in one zip that they can download to their system and then upload to their support ticket.

Currently, AWS Batch without Fargate & AWS Cloud CE are the only supported compute environments (CE) for Studios . Adding support for Microsoft Azure would benefit many customers who want to adopt interactive analyses within their Azure platform deployments.