Seqera Platform Feature Requests

When adding a new Studio, the "YAML list of formatted packages" input field should have additional inline help (e.g., a minimal working conda environment structure for each Seqera provided container template) to guide users because the YAML syntax is easy to forget. Having examples would reduce errors and improve usability.

Similar to the (undocumented?) query params for the quicklaunch pages: my.seqeracloud.com/quicklaunch?pipeline=https%3A%2F%2Fgithub.com%2Fnf-core%2Frnaseq&revision=3.15.1&paramsText=%7B%0D%0A++++%22input%22%3A+%22foo.csv%22%2C%0D%0A++++%22outdir%22%3A+%22bar%22%0D%0A%7D&resume=false Unfortunately with quicklaunch you cannot set the rest of the parameters anymore. We need it for the launchpad/12345678910/form page (which seems to be done with formly anyway which supports pre-filling if enabled correctly).

Users should be able to programmatically upload data in bulk (files and folders) to object storage in Data Explorer, and also download data in bulk from Data Explorer to their localhost .

As the number of users in a workspace increases, shared interactive environments can incur accidental edits. This can have serious downstream consequences if an interactive environment is part of a running data analysis pipeline or ML workflow (training a model, model in production, etc). To help avoid accidental edits, workspace Maintain+ role users (or just the creator) can lock the Studio session. This could be either: A one-way action (once locked, the session can never be unlocked). A lock/unlock action. Note: The audit log should capture this action for GxP compliance.

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

In the Launchpad when launching a pipeline when the input field has a long list of options add an type-ahead option to facilitate the search for required parameters.

At the moment if you want to fix a Nextflow version, you have to use a pre-run script to export the NXF_VER environment version. This is fine, but it's not intuitive for what is a fairly central part of the experience of running Nextflow on Seqera Platform. Suggestion is to have a new field in the UI to set the Nextflow version. This could potentially be when creating a new Compute Environment, ideally with a secondary field which could be set when launching a workflow (either to set new or to override the default in the CE). The field should default to using the latest stable release of Nextflow, but give the option of using the latest edge release instead, or a specified exact release version.

We would like to build custom launch interfaces for nf-core pipelines in our Seqera Platform instance. By that I mean a restricted, minimal interface that only allows to set a minimal set of parameters while the rest is either frozen to a predefined default, or derived from these parameters. For instance, for the nf-core/demultiplex pipeline, the only thing we'd like launch users to be able to set is the flowcell ID, the filename of the samplesheet and to which project this flowcell belongs. The input and output path shall be derived from the flowcell and project ID, and other options (e.g. demultiplexer ) shall not be editable by the user. For instance, to derived the outdir from the project_id , we'd envisage something like params.outdir = "s3://some-company-namespace-${params.project_id}/demultiplex" . To achieve this, for now, we built a custom Nextflow pipeline that wraps the nf-core pipeline with a custom schema. Example . However, ideally, the same could be achieved directly in Seqera Platform. For that, I believe the following would be necessary: support for custom schemas outside the pipeline repo, see also support for custom nextflow.config outside the pipeline repo some sort of scripting to manipulate params and possibly input samplesheets (i.e. generate params and samplesheets from whatever is specified in the custom schema).

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.

I would like to be able to edit an existing Compute Environment without the need to Clone and then make Primary again. It seems all options are greyed out once I try to open it to make changes. Resources can be changed on the fly in most cases on AWS. Being our environments are manual, we should be able to edit any piece as it will correspond to edits we have already made in the environment. This is especially important as we head into launching jobs from Seqera Platform. If I have 15 workflows, and I have to edit the CE, I now have to go through all workflows and change the CE. Imagine if we have 50 workflows?