Seqera Platform Feature Requests

Trusted research environments enabling research progress without sacrificing data security - ensuring data are handled in a secure and responsible manner. The following five general items need to be adhered to: Safe Data - Confidentiality of data is maintained Safe Projects - Data owners approve the research projects Safe People - Researchers are trained to use the data safely Safe Settings - A secure computing environment prevents unauthorised data access Safe Outputs - All exported results are screened and approved

Devcontainers is a standard format developed by Microsoft to configure development environments for VSCode and GitHub codespaces . It’s also going to be supported by GitPod . It’s a JSON file that sits in the root of a repo in a directory called .devcontainer/ . It can contain VSCode extensions, etc but the key things are: Dockerfile, docker arguments, and launch run commands. Supporting these files in Studios allow users to programmatically encode settings for Studios using a well adopted standard.

Currently, to interact with a Shiny/Dash/Streamlit dynamic dashboard you have to be connected to a running Studio session and manually execute the code, which typically opens a new browser window. The new application internal browser window creation process bypasses the current connect protocols and is therefore non-shareable. Making interactive dashboard URLs shareable across workspace participants would allow rapid feedback and iteration for notebook analyses/processes.

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

In the "About" tab of a completed task, it would be nice to have a link to launch a studio environment using the same image, and with the input data linked/copied into the environment. It would be a convenient way to quickly test different settings on a given step/tool.

It would be helpful from security and compliance perspectives to allow Enterprise installations of Seqera Platform to support custom subdomains for Studios.

For each of the various container template images (JupyterLab, RStudio, VSCode, Xpra), once a Studio session is in running state, allow users to run their local installation of the application but with the code and terminal running in the remote Studio session via a SSH tunnel. There is a VSCode plugin available that can be reviewed for inspiration.

Pipeline development in Nextflow is often done using docker. When inside a VS Code environment within Studios, I want to be able to run: nextflow run main.nf -with-docker The requirement is to run fast, "local" iterations rather than requiring an external service like AWS Batch or similar, which has delays.

We would like to store 3-5 pre-built docker images in the dropdown with custom, user-friendly names for each. Our users would much prefer to interact with known, user-friendly names rather than docker URIs.

Once a Studio session is running, it incurs costs. Estimating the hourly cost of the session and clearly presenting that in the user interface will ensure that users are aware of the potential cost impacts. The estimated hourly cost could initially be estimated on the “Add Studio” page (when the CE is selected) and be displayed on the specific Studio session detail page once the session is in a running state. When the session is in a stopped state, the cost estimator is still visible, but considered inactive.