Seqera Platform Feature Requests

I'd like to be able to chain pipelines together within Seqera Platform, and not rely on an external service such as lambda functions to chain demultiplex => rnaseq => differentialabundance together for example

When using tw-cli , seqerakit , or the Seqera Terraform Provider for deploying Compute Environments, there are many settings and most all of them independently toggle-able. If you want services like Wave and Fusion to work it's critical that you use the correct combinations of settings with the correct combinations of values for those settings. This can lead to validated CEs in small-batch testing, only to find with larger scale testing (when the users start running pipelines) that something is incorrectly configured. Seqera should host some clear, repeatable, and re-usable examples of full configurations for various use cases. Similar to how we have the Nextflow Patterns webpage that documents various end-to-end scripted methods for Nextflow, I feel that we really need something analogous for the Seqera Platform scripted deployments, because it's too easy to miss settings that you did not realize were required for your CE to work. I think some of the following would be good examples to start with, described in both tw-cli , seqerakit , and the Seqera Terraform Provider: deploying a Compute Environment with EBS AutoScale the above but with Wave included the above but with Wave + Fusion included launching a test pipeline on the CE just created above doing all of the above with both TowerForge created CE's and with Manually Added CE's I think some examples like this are already in the seqerakit GitHub repo, not sure if there are equivalents already available for tw-cli . Ultimately it will be needed for the Terraform Provider as well, and they will all benefit from being available in one place so that users can see everything at once.

We are currently exploring integration of Nextflow with various third-party systems, such as BaseSpace, Benchling and Slack so that, e.g. a pipeline could start by pulling data from BaseSpace using the BaseSpace API, combine that with meta-data from Benchling extracted using the Benchling API, and send various information/processing updates to Slack. This is all possible, but we have to pass in API keys into the pipeline for each of these applications, which we can currently only do by adding them in the Pipeline parameters section in Seqera Platform (we don't want to store them in our Docker containers or in GitHub for security reasons). We want to store these securely so that they can be configured in Seqera Platform by System Admins and passed into Nextflow scripts without being exposed through the platform interface, similar to how cloud and repo credentials currently get configured. It would be really useful if it were possible to add any generic type of credential/secret in the Credentials section in a workspace (probably made up of a name and any number of key-value pairs) and to then be able to use those credentials like params in a Nextflow script. Unlike params, they wouldn't be exposed on the Parameters or Configuration tabs. As an example, when adding credentials to a workspace in Seqera Platform, you could have another option, Other in the Provider drop-down which would enable you to create a credential record with the following fields (and this could get encrypted and stored): name : "benchling" token : "xyz" You could then reference that credential in a Nextflow script, something like this: $credentials.benchling.token The platform would pass those credentials to the script without exposing them on the Seqera Platform interface.

We'd like to be able to use Amazon EventBridge (previously called CloudWatch Events) for running cron jobs instead of running a docker container with cron in it.

We want a more secure approach to have the credentials in the configmap.yaml file be dynamically fetched from Azure key vault, instead of having them placed in clear text format.