From 203666733d8b0cd1dd0effc5b69a8461068e18bc Mon Sep 17 00:00:00 2001 From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 27 Feb 2025 12:40:53 +0000 Subject: [PATCH 1/8] Add namespace to secret creation heredoc --- platform_versioned_docs/version-24.1/compute-envs/k8s.mdx | 1 + 1 file changed, 1 insertion(+) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.mdx b/platform_versioned_docs/version-24.1/compute-envs/k8s.mdx index 04be2b206..ddf8103f7 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.mdx +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.mdx @@ -44,6 +44,7 @@ This guide applies a Kubernetes manifest that creates a service account named `t kind: Secret metadata: name: tower-launcher-token + namespace: tower-nf annotations: kubernetes.io/service-account.name: tower-launcher-sa type: kubernetes.io/service-account-token From 707b0f4611e7468fa084f64486f2b256d00c25cb Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 3 Jun 2025 22:58:24 +0200 Subject: [PATCH 2/8] Rename k8s.mdx to k8s.md Signed-off-by: Justine Geffen --- .../version-24.1/compute-envs/{k8s.mdx => k8s.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename platform_versioned_docs/version-24.1/compute-envs/{k8s.mdx => k8s.md} (100%) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.mdx b/platform_versioned_docs/version-24.1/compute-envs/k8s.md similarity index 100% rename from platform_versioned_docs/version-24.1/compute-envs/k8s.mdx rename to platform_versioned_docs/version-24.1/compute-envs/k8s.md From 8d8c88a3edd2383a03a574f46e3afef22f821b03 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 3 Jun 2025 23:02:55 +0200 Subject: [PATCH 3/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index ddf8103f7..8f0d6782a 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -114,7 +114,7 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c 1. Specify the **Namespace** created in the [cluster preparation](#cluster-preparation) instructions, which is _tower-nf_ by default. 1. Specify the **Head service account** created in the [cluster preparation](#cluster-preparation) instructions, which is _tower-launcher-sa_ by default. 1. Specify the **Storage claim** created in the [cluster preparation](#cluster-preparation) instructions, which serves as a scratch filesystem for Nextflow pipelines. The storage claim is called _tower-scratch_ in each of the provided examples. -1. Apply [**Resource labels**](../resource-labels/overview.mdx) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled. +1. Apply [**Resource labels**](../resource-labels/overview.md) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. From 7ffca8fb556099ca1fc343056fb6fa4c0471127f Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 3 Jun 2025 23:03:24 +0200 Subject: [PATCH 4/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index 8f0d6782a..0b85dcda3 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -125,7 +125,7 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c 1. Configure any advanced options described below, as needed. 1. Select **Create** to finalize the compute environment setup. -See [Launch pipelines](../launch/launchpad.mdx) to start executing workflows in your Kubernetes compute environment. +See [Launch pipelines](../launch/launchpad.md) to start executing workflows in your Kubernetes compute environment. ### Advanced options From be6cb6364679d530408bcdc4fc78d856d84caaff Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 7 Oct 2025 21:12:20 +0200 Subject: [PATCH 5/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index 0b85dcda3..895c4451f 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -54,7 +54,7 @@ This guide applies a Kubernetes manifest that creates a service account named `t 1. Confirm that Kubernetes created the persistent API token secret: ```bash - kubectl describe secrets/tower-launcher-token + kubectl -n tower-nf describe secrets/tower-launcher-token ``` 1. Create persistent storage. Seqera requires a `ReadWriteMany` persistent volume claim (PVC) mounted to all nodes where workflow pods will be dispatched. From 1512cb22967a348c8b073bda5acaba3e1ddc45d1 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Tue, 7 Oct 2025 21:12:28 +0200 Subject: [PATCH 6/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index 895c4451f..1317518c2 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -92,7 +92,7 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c - To authenticate using a Kubernetes service account, enter your **Service account token**. Obtain the token with the following command: ```bash - kubectl describe secret | grep -E '^token' | cut -f2 -d':' | tr -d '\t ' + kubectl -n tower-nf describe secret | grep -E '^token' | cut -f2 -d':' | tr -d '\t ' ``` Replace `` with the name of the service account token created in the [cluster preparation](#cluster-preparation) instructions (default: `tower-launcher-token`). From ac209dc45323b0649ddc33df576fe04b59eedcae Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Thu, 29 Jan 2026 15:54:35 +0200 Subject: [PATCH 7/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index 1317518c2..0503721ae 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -117,7 +117,7 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c 1. Apply [**Resource labels**](../resource-labels/overview.md) to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled. 1. Expand **Staging options** to include: - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. + - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. :::info Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. ::: From ede6d4e8d8968fd365793fd806c0588fb2b3bf03 Mon Sep 17 00:00:00 2001 From: Justine Geffen Date: Thu, 29 Jan 2026 15:54:43 +0200 Subject: [PATCH 8/8] Update platform_versioned_docs/version-24.1/compute-envs/k8s.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Signed-off-by: Justine Geffen --- platform_versioned_docs/version-24.1/compute-envs/k8s.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform_versioned_docs/version-24.1/compute-envs/k8s.md b/platform_versioned_docs/version-24.1/compute-envs/k8s.md index 0503721ae..0f9d11315 100644 --- a/platform_versioned_docs/version-24.1/compute-envs/k8s.md +++ b/platform_versioned_docs/version-24.1/compute-envs/k8s.md @@ -119,7 +119,7 @@ After you've prepared your Kubernetes cluster for Seqera integration, create a c - Optional [pre- or post-run Bash scripts](../launch/advanced.mdx#pre--post-run-scripts) that execute before or after the Nextflow pipeline execution in your environment. - Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the **Nextflow config file** field in the pipeline launch form. These values can be overridden during pipeline launch. :::info - Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. + Configuration settings in this field override the same values in the pipeline repository `nextflow.config` file. See [Nextflow config file](../launch/advanced.mdx#nextflow-config-file) for more information on configuration priority. ::: 1. You can use the **Environment variables** option to specify custom environment variables for the Head job and/or Compute jobs. 1. Configure any advanced options described below, as needed.