docs(seqera-ai): align Enterprise Co-Scientist docs for 26.1 by llewellyn-sl · Pull Request #1381 · seqeralabs/docs

llewellyn-sl · 2026-05-04T10:05:09Z

Summary

Align Platform Enterprise Co-Scientist docs with the Cloud docset for the Enterprise 26.1 release.
Add Enterprise guidance for skills, modes, coding-agent integrations, Nextflow LSP, projects, and usage/cost behavior.
Rewrite the Enterprise Seqera AI install page with current MCP, agent-backend, portal-web, Redis, MySQL, Bedrock, Anthropic direct, AgentCore, OIDC, and CLI guidance.

Validation

git diff --check
Parsed platform-enterprise_docs/enterprise-sidebar.json
Targeted stale-string scans for Cloud-only credits/install wording and old Helm chart paths.

Notes

This is the public-docs PR that should get the closest release-doc review.

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bebosudo · 2026-05-04T13:44:28Z

 ```bash
-export SEQERA_AUTH_DOMAIN=https://cloud.seqera.io/api
+export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
 export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli


Suggested change

export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli

this doesn't seem to be needed

I added these 4 to my shell when trying to get the CLI working. TBD if they were all necessary:

- `SEQERA_AI_BACKEND_URL` - `SEQERA_AUTH_DOMAIN` - `SEQERA_AUTH_CLI_CLIENT_ID` - `TOWER_ACCESS_TOKEN`

gwright99

Commented on the parts of this PR which touched upon deployment. I did not review the "how to use the CLI" since this was not part of my efforts last week.

gwright99 · 2026-05-04T14:03:47Z

- **Token encryption key** for encrypting sensitive tokens at rest. Generate with:
+- Seqera Platform Enterprise 26.1 or later deployed with the [Seqera Platform Helm chart](./platform-helm.md).
+- Helm v3 and `kubectl` installed locally.
+- DNS names and TLS certificates for the Platform, agent backend, MCP server, and portal web interface hosts.


If created manually, where are they getting the FQDNs from? Having to look at the Helm chart config?

bebosudo

Some initial recommendations, I've got some more coming up

Co-authored-by: Alberto Chiusole <1922124+bebosudo@users.noreply.github.com> Signed-off-by: Justine Geffen <justinegeffen@users.noreply.github.com>

justinegeffen · 2026-05-07T08:05:19Z

fix formatting

bebosudo · 2026-05-07T08:28:48Z

+      value: "false"
+```
+
+Documentation search embeddings are independent from chat inference. Keep Titan embeddings configured through Bedrock when you use improved documentation search.


Adding this note here as a reminder to update the docs after we update the helm charts and define the inference provider and documentation index user-interface (i.e. there should be no need to specify values via extraEnvVars). cc @endre-seqera

bebosudo · 2026-05-07T08:29:39Z

+Configure Bedrock so Claude inference and Titan embeddings run in your AWS account. Bedrock is the recommended Enterprise configuration.
+
+```yaml
+agent-backend:


I'm not sure specifying agent-backend may be misleading to users, and I need to test what happens when the same map is specified multiple times, does it augment the previous one or overwrite it?

bebosudo · 2026-05-07T08:35:41Z

+  enabled: true
+```
+
+Expose MCP, agent backend, and portal web through the chart ingress only if you use Kubernetes Ingress. If you use the Gateway API or another network layer, configure that layer instead.


This sentence should go at the top of the document probably, and made less redundant possibly, something like "The MCP, agent backend and portal web Helm charts provide the option to define kubernetes ingresses: other methods to expose the services can be used, e.g. via the extraDeploy resource".

bebosudo · 2026-05-07T08:43:10Z

+
+Enterprise deployments do not use Seqera Cloud credit balances or the Cloud credit request flow. Usage and inference costs are managed by your organization through the configured inference provider, such as AWS Bedrock or Anthropic API.
+
+When `ORG_CREDITS_ENABLED=false` is set on the agent backend deployment, the CLI `/credits` command reports that usage is managed by your organization and directs users to their Seqera administrator.


I want to bring this value into the helm chart if it's important to enterprise customers so they won't need to play with extraEnvVars

this is now set to false for the new builds, let's remove it

Suggested change

When `ORG_CREDITS_ENABLED=false` is set on the agent backend deployment, the CLI `/credits` command reports that usage is managed by your organization and directs users to their Seqera administrator.

justinegeffen · 2026-05-11T13:54:08Z

Should we add https://docs.seqera.io/platform-enterprise/seqera-ai/prerequisites to the LHS in this PR? @gavinelder, @odagayev?

Co-authored-by: Alberto Chiusole <1922124+bebosudo@users.noreply.github.com> Signed-off-by: Justine Geffen <justinegeffen@users.noreply.github.com>

Signed-off-by: Justine Geffen <justinegeffen@users.noreply.github.com>

bebosudo reviewed May 4, 2026

View reviewed changes

gwright99 reviewed May 4, 2026

View reviewed changes

justinegeffen changed the base branch from master to enterprise-26.1-documentation May 4, 2026 14:23

llewellyn-sl force-pushed the 26-1-docs-update branch from 239f207 to 403a157 Compare May 4, 2026 18:28