From f4b9f00a89b128b6ab20dc59185b7f73cb3ad81a Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Sun, 11 May 2025 13:31:08 +0200 Subject: [PATCH 1/4] Update netlify.toml --- netlify.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/netlify.toml b/netlify.toml index 46d5381a7..6a4e83954 100644 --- a/netlify.toml +++ b/netlify.toml @@ -9,7 +9,7 @@ # Default production branch - exclude enterprise docs (includes API docs) [context.master.environment] EXCLUDE_PLATFORM_API="0" - EXCLUDE_PLATFORM_OPENAPI="10" + EXCLUDE_PLATFORM_OPENAPI="0" # Testing only - dev branch excluding enterprise docs (can be removed after #594 is live) [context.exclude-apidocs.environment] From ad0357a95d56df09b78693e9b258d7f78c398e85 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Tue, 3 Jun 2025 14:56:02 +0200 Subject: [PATCH 2/4] Config view -> Params file view --- .../getting-started/quickstart-demo/launch-pipelines.mdx | 2 +- .../version-23.4/getting-started/rnaseq.mdx | 2 +- .../version-24.1/getting-started/proteinfold.mdx | 2 +- .../getting-started/quickstart-demo/comm-showcase.mdx | 2 +- .../getting-started/quickstart-demo/launch-pipelines.mdx | 2 +- .../version-24.1/getting-started/rnaseq.mdx | 2 +- .../version-24.1/launch/launchpad.md | 2 +- .../version-24.2/getting-started/proteinfold.mdx | 2 +- .../getting-started/quickstart-demo/comm-showcase.mdx | 2 +- .../getting-started/quickstart-demo/launch-pipelines.mdx | 2 +- .../version-24.2/getting-started/rnaseq.mdx | 2 +- .../version-24.2/launch/launchpad.md | 2 +- .../version-25.1/getting-started/proteinfold.md | 2 +- .../getting-started/quickstart-demo/comm-showcase.md | 2 +- .../getting-started/quickstart-demo/launch-pipelines.md | 2 +- .../version-25.1/getting-started/rnaseq.md | 2 +- .../version-25.1/launch/launchpad.md | 2 +- 17 files changed, 17 insertions(+), 17 deletions(-) diff --git a/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx b/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx index 4ffc3cdae..e97fc8702 100644 --- a/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx +++ b/platform-enterprise_versioned_docs/version-23.4/getting-started/quickstart-demo/launch-pipelines.mdx @@ -63,7 +63,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Specify your pipeline input and output and modify other pipeline parameters as needed: diff --git a/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx index 0fa590391..9a16223c0 100644 --- a/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx @@ -215,7 +215,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx index 8e9f45370..54414427a 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/proteinfold.mdx @@ -203,7 +203,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/comm-showcase.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/comm-showcase.mdx index fdbfc882a..5b4dd50a5 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/comm-showcase.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/comm-showcase.mdx @@ -67,7 +67,7 @@ Most Community Showcase pipeline parameters are prefilled. Specify the following There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. #### input diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.mdx index 4ffc3cdae..e97fc8702 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/launch-pipelines.mdx @@ -63,7 +63,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Specify your pipeline input and output and modify other pipeline parameters as needed: diff --git a/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx index 6124bd693..16ef78e41 100644 --- a/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx @@ -215,7 +215,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md b/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md index 5214a26f6..06f375031 100644 --- a/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-24.1/launch/launchpad.md @@ -52,7 +52,7 @@ For saved pipelines, **General config** and **Run parameters** fields are prefil There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Seqera uses a `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. Most pipelines contain at least input and output parameters: diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx index 8e9f45370..54414427a 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/proteinfold.mdx @@ -203,7 +203,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/comm-showcase.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/comm-showcase.mdx index fb3a86a24..4130ec351 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/comm-showcase.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/comm-showcase.mdx @@ -66,7 +66,7 @@ Most Showcase pipeline parameters are prefilled. Specify the following fields to There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. #### input diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.mdx index 4ffc3cdae..e97fc8702 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/quickstart-demo/launch-pipelines.mdx @@ -63,7 +63,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Specify your pipeline input and output and modify other pipeline parameters as needed: diff --git a/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx b/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx index 6124bd693..16ef78e41 100644 --- a/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx +++ b/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx @@ -215,7 +215,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md b/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md index 9ade4dea2..22530a830 100644 --- a/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-24.2/launch/launchpad.md @@ -86,7 +86,7 @@ The dropdown of available config profiles is populated by inspecting the Nextflo There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Seqera uses a `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. Most pipelines contain at least input and output parameters: diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.md index ce56a180c..31444a438 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/proteinfold.md @@ -202,7 +202,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/comm-showcase.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/comm-showcase.md index 6be0c679f..514d8c776 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/comm-showcase.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/comm-showcase.md @@ -66,7 +66,7 @@ Most Showcase pipeline parameters are prefilled. Specify the following fields to There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. #### input diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md index 4ffc3cdae..e97fc8702 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/quickstart-demo/launch-pipelines.md @@ -63,7 +63,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Specify your pipeline input and output and modify other pipeline parameters as needed: diff --git a/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.md b/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.md index 3f3cf0948..73649c6d1 100644 --- a/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.md +++ b/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.md @@ -215,7 +215,7 @@ The launch form consists of **General config**, **Run parameters**, and **Advanc There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text or select attributes from lists, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays raw configuration text that you can edit directly. Select JSON or YAML format from the **View as** list. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** list. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Platform uses the `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. diff --git a/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md b/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md index ce98f508a..f7dfb8e8a 100644 --- a/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md +++ b/platform-enterprise_versioned_docs/version-25.1/launch/launchpad.md @@ -86,7 +86,7 @@ The dropdown of available config profiles is populated by inspecting the Nextflo There are three ways to enter **Run parameters** prior to launch: - The **Input form view** displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with [Data Explorer](../data/data-explorer). -- The **Config view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. +- The **Params file view** displays a raw schema that you can edit directly. Select JSON or YAML format from the **View as** dropdown. - **Upload params file** allows you to upload a JSON or YAML file with run parameters. Seqera uses a `nextflow_schema.json` file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. Most pipelines contain at least input and output parameters: From 33f8469f3ddd7cc50a65270fbe2abe842c295b3d Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 21 Jan 2026 15:39:22 +0200 Subject: [PATCH 3/4] Restore claude-generated-overlays.md for workflow re-run The file was archived by the workflow after successful completion. Restoring it so the workflow can be triggered again to regenerate the correct MDX files with all the fixes applied. Restored from commit 038135de which contains all 14 overlays: - add-missing-schema-overlay-1.102.0.yaml - add-identities-tag-overlay-1.102.0.yaml - compute-envs-operations-overlay-1.102.0.yaml - compute-envs-parameters-overlay-1.102.0.yaml - compute-envs-schemas-overlay-1.102.0.yaml - data-links-operations-overlay-1.102.0.yaml - data-links-parameters-overlay-1.102.0.yaml - workflows-parameters-overlay-1.102.0.yaml - workflows-operations-overlay-1.102.0.yaml - global-schemas-overlay-1.102.0.yaml - manual-field-descriptions-overlay-1.102.0.yaml - fix-duplicate-required-fields-overlay-1.102.0.yaml - fix-duplicate-enums-overlay-1.102.0.yaml - remove-google-lifesciences-overlay-1.102.0.yaml Co-Authored-By: Claude Sonnet 4.5 --- .../specs/claude-generated-overlays.md | 1227 +++++++++++++++++ 1 file changed, 1227 insertions(+) create mode 100644 platform-api-docs/scripts/specs/claude-generated-overlays.md diff --git a/platform-api-docs/scripts/specs/claude-generated-overlays.md b/platform-api-docs/scripts/specs/claude-generated-overlays.md new file mode 100644 index 000000000..2afaff260 --- /dev/null +++ b/platform-api-docs/scripts/specs/claude-generated-overlays.md @@ -0,0 +1,1227 @@ +# Generated Overlays for v1.102.0 + +This file contains all the overlay files generated from the base-1.95-to-1.102.0-changes.yaml comparison overlay, plus manual enrichments for field descriptions. + +**CRITICAL FIXES**: +- `data-links-operations-overlay-1.102.0.yaml` now correctly REMOVES the deprecated `/data-links/{dataLinkId}/download` endpoint +- `data-links-parameters-overlay-1.102.0.yaml` includes parameter array removal actions to prevent duplicate parameters + +--- + +# Missing Schemas (Must Apply First) + +## add-missing-schema-overlay-1.102.0.yaml + +**CRITICAL**: This schema exists in v1.95 base spec but was accidentally excluded from v1.95 decorated spec. Must be added BEFORE other overlays can reference it in ComputeConfig.oneOf array. + +```yaml +overlay: 1.0.0 +info: + title: Add missing LocalComputeConfig schema + version: 1.102.0 +actions: + # ===== ADD MISSING LocalComputeConfig SCHEMA ===== + + # This schema exists in v1.95 base spec but was accidentally excluded from v1.95 decorated spec + # We need to add it before other overlays can reference it + + - target: "$.components.schemas" + update: + LocalComputeConfig: + type: object + title: Local execution configuration + properties: + workDir: + type: string + description: "Compute environment working directory." + preRunScript: + type: string + description: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + postRunScript: + type: string + description: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + environment: + type: array + description: "Array of environment variables for the compute environment." + items: + $ref: "#/components/schemas/ConfigEnvVariable" + nextflowConfig: + type: string + description: "Additional Nextflow configuration content." + discriminator: + type: string + description: "Property to select the compute config platform." + readOnly: true + waveEnabled: + type: boolean + description: "Enable Wave containers support. See [Wave containers](https://docs.seqera.io/platform-cloud/supported_software/wave)." + fusion2Enabled: + type: boolean + description: "Enable Fusion v2 virtual distributed file system. See [Fusion file system](https://docs.seqera.io/platform-cloud/supported_software/fusion)." +``` + +--- + +# Compute Environments Overlays + +## compute-envs-operations-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Compute environments operations overlay + version: 0.0.0 +actions: + # ===== COMPUTE ENVIRONMENTS - OPERATIONS ===== + + # ---- DISABLE COMPUTE ENVIRONMENT ---- + + - target: "$.paths./compute-envs/{computeEnvId}/disable.post.summary" + update: "Disable compute environment" + + - target: "$.paths./compute-envs/{computeEnvId}/disable.post.description" + update: "Disables the compute environment identified by the given `computeEnvId`. A disabled compute environment cannot be used to launch new workflows or Studio sessions. If the compute environment is primary, it will be automatically unset as primary. See [Disable compute environment](https://docs.seqera.io/platform-cloud/compute-envs/overview#disable-compute-environment)" + + # ---- ENABLE COMPUTE ENVIRONMENT ---- + + - target: "$.paths./compute-envs/{computeEnvId}/enable.post.summary" + update: "Enable compute environment" + + - target: "$.paths./compute-envs/{computeEnvId}/enable.post.description" + update: "Enables the compute environment identified by the given `computeEnvId`. An enabled compute environment can be used to launch new workflows and Studio sessions." +``` + +## compute-envs-parameters-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Compute environments parameters overlay + version: 0.0.0 +actions: + # ===== COMPUTE ENVIRONMENTS PARAMETERS - PATH, QUERY, AND REQUEST BODY ===== + + # ---- DISABLE COMPUTE ENVIRONMENT PARAMETERS ---- + + - target: "$.paths./compute-envs/{computeEnvId}/disable.post.parameters[?(@.name=='computeEnvId')].description" + update: "Compute environment string identifier." + + - target: "$.paths./compute-envs/{computeEnvId}/disable.post.parameters[?(@.name=='workspaceId')].description" + update: "Workspace numeric identifier." + + - target: "$.paths./compute-envs/{computeEnvId}/disable.post.requestBody.description" + update: "Compute environment disable request" + + # ---- ENABLE COMPUTE ENVIRONMENT PARAMETERS ---- + + - target: "$.paths./compute-envs/{computeEnvId}/enable.post.parameters[?(@.name=='computeEnvId')].description" + update: "Compute environment string identifier." + + - target: "$.paths./compute-envs/{computeEnvId}/enable.post.parameters[?(@.name=='workspaceId')].description" + update: "Workspace numeric identifier." + + - target: "$.paths./compute-envs/{computeEnvId}/enable.post.requestBody.description" + update: "Compute environment enable request" +``` + +## compute-envs-schemas-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Compute environments schemas overlay + version: 0.0.0 +actions: + # ===== COMPUTE ENVIRONMENTS SCHEMAS - REQUEST/RESPONSE OBJECTS ===== + + # ---- COMPUTE ENVIRONMENT STATUS ENUM ---- + + - target: "$.components.schemas.ComputeEnv.Status" + update: + type: string + enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID", "DISABLED"] + description: "Compute environment status. Accepts `CREATING`, `AVAILABLE`, `ERRORED`, `INVALID`, or `DISABLED`." +``` + +--- + +# Data Links Overlays + +## data-links-operations-overlay-1.102.0.yaml + +```yaml +actions: + # ===== DATA-LINKS - OPERATIONS ===== + + # Update existing operations + + - target: "$.paths./data-links/{dataLinkId}/browse.get.summary" + update: "Explore data-link" + + - target: "$.paths./data-links/{dataLinkId}/browse.get.description" + update: "Retrieves the content of the data-link associated with the given `dataLinkId`." + + - target: "$.paths./data-links/{dataLinkId}/browse/{path}.get.operationId" + update: "ExploreDataLinkWithPath" + + - target: "$.paths./data-links/{dataLinkId}/upload.post.summary" + update: "Generate data-link file upload URL" + + - target: "$.paths./data-links/{dataLinkId}/upload.post.description" + update: "Creates a URL to upload files to the data-link associated with the given `dataLinkId`. For AWS S3 data-links, an additional follow-up request must be sent after your file upload has completed (or encountered an error) to finalize the upload - see the `/upload/finish` endpoint." + + - target: "$.paths./data-links/{dataLinkId}/upload/{dirPath}.post.operationId" + update: "GenerateDataLinkUploadUrlWithPath" + + - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.summary" + update: "Finish data-link file upload" + + - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.description" + update: "Finish upload of a data-link file. This is necessary for AWS S3 data-links (`DataLinkProvider=aws`) to finalize a successful file upload, or abort an upload if an error was encountered while uploading a file using an upload URL from the `/upload` endpoint." + + - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.responses['404'].description" + update: "NotFound — workspace or credentials not found, API disabled for the workspace, or data-link not found." + + - target: "$.paths./data-links/{dataLinkId}/upload/finish/{dirPath}.post.operationId" + update: "FinishDataLinkUploadWithPath" + + - target: "$.paths./data-links/{dataLinkId}/upload/finish/{dirPath}.post.responses['200'].description" + update: "FinishDataLinkUploadWithPath 200 response." + + # New endpoint in v1.102.0 + + - target: "$.paths" + update: + /data-links/{dataLinkId}/download/{filePath}: + get: + tags: + - data-links + summary: "Download data-link file at path" + description: "Downloads the content at the given `filePath` in the data-link associated with the given `dataLinkId`." + operationId: DownloadDataLink + parameters: + - name: dataLinkId + in: path + description: "Data-link string identifier." + required: true + schema: + type: string + - name: filePath + in: path + description: "Resource path of the file to download." + required: true + schema: + type: string + - name: credentialsId + in: query + description: "Credentials string identifier." + schema: + type: string + - name: workspaceId + in: query + description: "Workspace numeric identifier." + schema: + type: integer + format: int64 + responses: + "200": + description: "OK." + content: + application/json: + schema: + type: string + format: binary + "400": + description: "Bad request." + content: + application/json: + schema: + $ref: "#/components/schemas/ErrorResponse" + "404": + description: "NotFound — workspace or credentials not found, API disabled for the workspace, or data-link or path not found." + content: + application/json: + schema: + $ref: "#/components/schemas/ErrorResponse" + "403": + description: "Operation not allowed." + security: + - BearerAuth: [] + + # Remove deprecated endpoint + + - target: "$.paths./data-links/{dataLinkId}/download" + remove: true +``` + +## data-links-parameters-overlay-1.102.0.yaml + +**CRITICAL**: This overlay includes parameter array removal actions to prevent duplicate parameters. + +```yaml +overlay: 1.0.0 +info: + title: Data-links parameters overlay + version: 1.102.0 +actions: + # ===== DATA-LINKS PARAMETERS ===== + + # ---- /data-links/{dataLinkId}/browse GET ---- + + # CRITICAL: Remove entire parameters array to prevent duplicates + - target: "$.paths./data-links/{dataLinkId}/browse.get.parameters[*]" + remove: true + + # Replace with complete array with enriched descriptions + - target: "$.paths./data-links/{dataLinkId}/browse.get.parameters" + update: + - name: dataLinkId + in: path + description: "Data-link string identifier." + required: true + schema: + type: string + - name: workspaceId + in: query + description: "Workspace numeric identifier." + schema: + type: integer + format: int64 + - name: credentialsId + in: query + description: "Credentials string identifier." + schema: + type: string + - name: search + in: query + description: "Prefix search of data-link content." + schema: + type: string + - name: nextPageToken + in: query + description: "Token used to fetch the next page of items." + schema: + type: string + - name: pageSize + in: query + description: "Number of items to return per page. If omitted, a default maximum value is returned." + schema: + type: integer + format: int32 + + # ---- /data-links/{dataLinkId}/upload POST ---- + + # CRITICAL: Remove entire parameters array to prevent duplicates + - target: "$.paths./data-links/{dataLinkId}/upload.post.parameters[*]" + remove: true + + # Replace with complete array with enriched descriptions + - target: "$.paths./data-links/{dataLinkId}/upload.post.parameters" + update: + - name: dataLinkId + in: path + description: "Data-link string identifier." + required: true + schema: + type: string + - name: credentialsId + in: query + description: "Credentials string identifier." + schema: + type: string + - name: workspaceId + in: query + description: "Workspace numeric identifier." + schema: + type: integer + format: int64 + - name: Origin + in: header + schema: + type: string + nullable: true + + # ---- /data-links/{dataLinkId}/upload/finish POST ---- + + # CRITICAL: Remove entire parameters array to prevent duplicates + - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.parameters[*]" + remove: true + + # Replace with complete array with enriched descriptions + - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.parameters" + update: + - name: dataLinkId + in: path + description: "Data-link string identifier." + required: true + schema: + type: string + - name: credentialsId + in: query + description: "Credentials string identifier." + schema: + type: string + - name: workspaceId + in: query + description: "Workspace numeric identifier." + schema: + type: integer + format: int64 +``` + +--- + +# Workflows Overlays + +## workflows-parameters-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Workflows parameters overlay + version: 0.0.0 +actions: + # ===== WORKFLOWS PARAMETERS - QUERY PARAMETERS ===== + + # ---- LIST WORKFLOWS PARAMETERS ---- + + - target: "$.paths./workflow.get.parameters[?(@.name=='includeTotalSize')].description" + update: "If true, includes total result count in the response. Default: `false`." +``` + +## workflows-operations-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Workflows operations overlay + version: 0.0.0 +actions: + # ===== WORKFLOWS - OPERATIONS ===== + + # ---- LAUNCH WORKFLOW ---- + + - target: "$.paths./workflow/launch.post.description" + update: | + Submits a workflow execution. + + **To [resume](https://docs.seqera.io/platform-cloud/launch/cache-resume#resume-a-workflow-run) a workflow**: First, retrieve the launch configuration using [`GET /workflow/{workflowId}/launch`](https://docs.seqera.io/platform-api/describe-workflow-launch). Then modify the response by setting `workDir` to the value from `resumeDir`, `revision` to the value from `resumeCommitId`, and `resume` to `true`. Submit the modified payload to this endpoint to resume the workflow. +``` + +--- + +# Global Schemas Overlay + +## global-schemas-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Global schemas overlay + version: 0.0.0 +actions: + # ===== GLOBAL SCHEMAS - CREDENTIALS AND COMPUTE CONFIGURATIONS ===== + + # ---- GIT CREDENTIALS ---- + + - target: "$.components.schemas.GitKeys.description" + update: "Git repository credentials." + + - target: "$.components.schemas.GitKeys.properties.discriminator.description" + update: "Property to select the credentials type." + + - target: "$.components.schemas.GitKeys.properties.username.description" + update: "Git username for authentication." + + - target: "$.components.schemas.GitKeys.properties.password.description" + update: "Git password for authentication." + + - target: "$.components.schemas.GitKeys.properties.token.description" + update: "Git personal access token for authentication." + + # ---- SEQERA COMPUTE CLOUD INSTANCE TYPE SIZE ---- + + - target: "$.components.schemas.SeqeraComputeCloudInstanceTypeSize.description" + update: "Data Studios instance size. Accepts `SMALL`, `MEDIUM`, or `LARGE`." + + # ---- SEQERA COMPUTE CONFIG ---- + + - target: "$.components.schemas.SeqeraComputeConfig.properties.instanceTypeSize.description" + update: "Size of the Data Studios instance. Accepts `SMALL`, `MEDIUM`, or `LARGE`." + + # ---- ABSTRACT GRID CONFIG ---- + + - target: "$.components.schemas.AbstractGridConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.AbstractGridConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.AbstractGridConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.AbstractGridConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.AbstractGridConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.AbstractGridConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.AbstractGridConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.AbstractGridConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.AbstractGridConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.AbstractGridConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.AbstractGridConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.AbstractGridConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.AbstractGridConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.AbstractGridConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.AbstractGridConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + # ---- LSF COMPUTE CONFIG ---- + + - target: "$.components.schemas.LsfComputeConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.LsfComputeConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.LsfComputeConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.LsfComputeConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.LsfComputeConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.LsfComputeConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.LsfComputeConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.LsfComputeConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.LsfComputeConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.LsfComputeConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.LsfComputeConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.LsfComputeConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.LsfComputeConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.LsfComputeConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.LsfComputeConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + - target: "$.components.schemas.LsfComputeConfig.properties.unitForLimits.description" + update: "Unit for memory and time limits in LSF." + + - target: "$.components.schemas.LsfComputeConfig.properties.perJobMemLimit.description" + update: "If true, applies memory limit per job. Default: `false`." + + - target: "$.components.schemas.LsfComputeConfig.properties.perTaskReserve.description" + update: "If true, reserves resources per task. Default: `false`." + + # ---- SLURM COMPUTE CONFIG ---- + + - target: "$.components.schemas.SlurmComputeConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.SlurmComputeConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.SlurmComputeConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.SlurmComputeConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.SlurmComputeConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.SlurmComputeConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.SlurmComputeConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.SlurmComputeConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.SlurmComputeConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.SlurmComputeConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.SlurmComputeConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.SlurmComputeConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.SlurmComputeConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.SlurmComputeConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.SlurmComputeConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + # ---- ALTAIR PBS COMPUTE CONFIG ---- + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.AltairPbsComputeConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + # ---- MOAB COMPUTE CONFIG ---- + + - target: "$.components.schemas.MoabComputeConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.MoabComputeConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.MoabComputeConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.MoabComputeConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.MoabComputeConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.MoabComputeConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.MoabComputeConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.MoabComputeConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.MoabComputeConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.MoabComputeConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.MoabComputeConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.MoabComputeConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.MoabComputeConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.MoabComputeConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.MoabComputeConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + # ---- UNIVA COMPUTE CONFIG ---- + + - target: "$.components.schemas.UnivaComputeConfig.properties.workDir.description" + update: "Compute environment working directory." + + - target: "$.components.schemas.UnivaComputeConfig.properties.preRunScript.description" + update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.UnivaComputeConfig.properties.postRunScript.description" + update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." + + - target: "$.components.schemas.UnivaComputeConfig.properties.environment.description" + update: "Array of environment variables for the compute environment." + + - target: "$.components.schemas.UnivaComputeConfig.properties.nextflowConfig.description" + update: "Additional Nextflow configuration content." + + - target: "$.components.schemas.UnivaComputeConfig.properties.discriminator.description" + update: "Property to select the compute config platform." + + - target: "$.components.schemas.UnivaComputeConfig.properties.launchDir.description" + update: "Launch directory for Nextflow execution." + + - target: "$.components.schemas.UnivaComputeConfig.properties.userName.description" + update: "Username for SSH authentication to the HPC cluster." + + - target: "$.components.schemas.UnivaComputeConfig.properties.hostName.description" + update: "Hostname or IP address of the HPC cluster head node." + + - target: "$.components.schemas.UnivaComputeConfig.properties.port.description" + update: "SSH port for connecting to the HPC cluster. Default: `22`." + + - target: "$.components.schemas.UnivaComputeConfig.properties.headQueue.description" + update: "Queue name for submitting the Nextflow head job." + + - target: "$.components.schemas.UnivaComputeConfig.properties.computeQueue.description" + update: "Queue name for submitting Nextflow compute jobs." + + - target: "$.components.schemas.UnivaComputeConfig.properties.maxQueueSize.description" + update: "Maximum number of jobs that can be queued at one time." + + - target: "$.components.schemas.UnivaComputeConfig.properties.headJobOptions.description" + update: "Additional options for the head job submission." + + - target: "$.components.schemas.UnivaComputeConfig.properties.propagateHeadJobOptions.description" + update: "If true, head job options are propagated to compute jobs. Default: `false`." + + # ---- EKS COMPUTE CONFIG ---- + + - target: "$.components.schemas.EksComputeConfig.properties.region.description" + update: "AWS region where the EKS cluster is located." + + - target: "$.components.schemas.EksComputeConfig.properties.clusterName.description" + update: "Name of the AWS EKS cluster." + + # ---- GKE COMPUTE CONFIG ---- + + - target: "$.components.schemas.GkeComputeConfig.properties.region.description" + update: "Google Cloud region or zone where the GKE cluster is located." + + - target: "$.components.schemas.GkeComputeConfig.properties.clusterName.description" + update: "Name of the Google GKE cluster." + + # ---- WORKFLOW AND TASK SCHEMAS ---- + + - target: "$.components.schemas.Task.properties.numSpotInterruptions.description" + update: "Number of spot instance interruptions encountered by this task." + + - target: "$.components.schemas.TraceProgressData.properties.numSpotInterruptions.description" + update: "Total number of spot instance interruptions across all tasks." + + - target: "$.components.schemas.WorkflowLoad.properties.numSpotInterruptions.description" + update: "Number of spot instance interruptions for the workflow." + + # ---- LIST WORKFLOWS RESPONSE ---- + + - target: "$.components.schemas.ListWorkflowsResponse.properties.hasMore.description" + update: "If true, indicates there are more results available beyond this page." + + # ---- ORGANIZATION QUOTAS ---- + + - target: "$.components.schemas.OrganizationQuotas.properties.maxCustomRolesPerOrg.description" + update: "Maximum number of custom roles allowed per organization." + + # ---- DATA STUDIO STOP REASON ---- + + - target: "$.components.schemas.DataStudioStopReason.description" + update: "Reason for Data Studio session termination. Accepts `UNKNOWN`, `USER_REQUEST`, `TIMEOUT`, `ERROR`, `RESOURCE_LIMIT`, or `NO_STATS_AVAIL`." +``` + +--- + +# Manual Field Descriptions Overlay + +## manual-field-descriptions-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Manual field descriptions overlay + version: 0.0.0 +actions: + # ===== PIPELINE SECRETS SCHEMAS ===== + + # ---- CREATE PIPELINE SECRET REQUEST ---- + + - target: "$.components.schemas.CreatePipelineSecretRequest.properties.name.description" + update: "Unique name for the pipeline secret within the workspace. Used to reference the secret in workflow configurations." + + - target: "$.components.schemas.CreatePipelineSecretRequest.properties.value.description" + update: "The secret value to be securely stored. This value will be made available to pipeline executions as an environment variable or configuration value." + + # ---- UPDATE PIPELINE SECRET REQUEST ---- + + - target: "$.components.schemas.UpdatePipelineSecretRequest.properties.value.description" + update: "New secret value to replace the existing value. The secret value is securely stored and made available to pipeline executions." + + # ===== DATASETS SCHEMAS ===== + + # ---- CREATE DATASET REQUEST ---- + + - target: "$.components.schemas.CreateDatasetRequest.properties.name.description" + update: "Unique dataset name within the workspace. Must be a valid identifier that can be referenced in workflow configurations." + + - target: "$.components.schemas.CreateDatasetRequest.properties.description.description" + update: "Optional description of the dataset. Provides context about the dataset contents, source, or intended use." + + # ---- UPDATE DATASET REQUEST ---- + + - target: "$.components.schemas.UpdateDatasetRequest.properties.name.description" + update: "New name for the dataset. Must be unique within the workspace and can be used to reference the dataset in workflow configurations." + + - target: "$.components.schemas.UpdateDatasetRequest.properties.description.description" + update: "Updated description for the dataset. Provides context about the dataset contents, source, or intended use." + + # ===== WORKSPACES SCHEMAS ===== + + # ---- UPDATE WORKSPACE REQUEST ---- + + - target: "$.components.schemas.UpdateWorkspaceRequest.properties.name.description" + update: "New short name for the workspace. Must be 2-40 characters, start and end with alphanumeric characters, and can contain hyphens or underscores between characters. Must be unique within the organization." + + - target: "$.components.schemas.UpdateWorkspaceRequest.properties.fullName.description" + update: "Updated full display name for the workspace. Maximum 100 characters." + + - target: "$.components.schemas.UpdateWorkspaceRequest.properties.description.description" + update: "Updated description of the workspace. Maximum 1000 characters." + + # ===== ACTIONS SCHEMAS ===== + + # ---- UPDATE ACTION REQUEST ---- + + - target: "$.components.schemas.UpdateActionRequest.properties.name.description" + update: "New name for the pipeline action. Must be unique within the workspace." +``` + +--- + +# Fix Duplicate Required Fields Overlay + +## fix-duplicate-required-fields-overlay-1.102.0.yaml + +**CRITICAL**: This overlay fixes duplicate required fields in compute config schemas using the "remove first, then update" pattern. + +```yaml +overlay: 1.0.0 +info: + title: Fix duplicate required fields overlay + version: 1.102.0 +actions: + # ===== FIX DUPLICATE REQUIRED FIELDS ===== + + # These duplicate required fields exist in the base spec + # We use the "remove first, then update" pattern to fix them + + # ---- AwsBatchConfig ---- + + - target: "$.components.schemas.AwsBatchConfig.required" + remove: true + + - target: "$.components.schemas.AwsBatchConfig" + update: + required: ["region", "workDir"] + + # ---- AwsCloudConfig ---- + + - target: "$.components.schemas.AwsCloudConfig.required" + remove: true + + - target: "$.components.schemas.AwsCloudConfig" + update: + required: ["region", "workDir"] + + # ---- AzBatchConfig ---- + + - target: "$.components.schemas.AzBatchConfig.required" + remove: true + + - target: "$.components.schemas.AzBatchConfig" + update: + required: ["region", "workDir"] + + # ---- AzCloudConfig ---- + + - target: "$.components.schemas.AzCloudConfig.required" + remove: true + + - target: "$.components.schemas.AzCloudConfig" + update: + required: ["location", "workDir"] + + # ---- ConfigEnvVariable ---- + + - target: "$.components.schemas.ConfigEnvVariable.required" + remove: true + + - target: "$.components.schemas.ConfigEnvVariable" + update: + required: ["name", "value"] + + # ---- CreateComputeEnvRequest ---- + + - target: "$.components.schemas.CreateComputeEnvRequest.required" + remove: true + + - target: "$.components.schemas.CreateComputeEnvRequest" + update: + required: ["computeEnv"] + + # ---- GkeComputeConfig ---- + + - target: "$.components.schemas.GkeComputeConfig.required" + remove: true + + - target: "$.components.schemas.GkeComputeConfig" + update: + required: ["region", "clusterName", "workDir"] + + # ---- GoogleBatchConfig ---- + + - target: "$.components.schemas.GoogleBatchConfig.required" + remove: true + + - target: "$.components.schemas.GoogleBatchConfig" + update: + required: ["location", "workDir"] + + # ---- GoogleCloudConfig ---- + + - target: "$.components.schemas.GoogleCloudConfig.required" + remove: true + + - target: "$.components.schemas.GoogleCloudConfig" + update: + required: ["region", "workDir"] + + # ---- K8sComputeConfig ---- + + - target: "$.components.schemas.K8sComputeConfig.required" + remove: true + + - target: "$.components.schemas.K8sComputeConfig" + update: + required: ["server", "sslCert", "workDir"] + + # ---- SeqeraComputeConfig ---- + + - target: "$.components.schemas.SeqeraComputeConfig.required" + remove: true + + - target: "$.components.schemas.SeqeraComputeConfig" + update: + required: ["region", "workDir"] + + # ---- ComputeEnv_ComputeConfig_ ---- + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_.required" + remove: true + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_" + update: + required: ["config", "name", "platform"] + + # ---- EksComputeConfig ---- + + - target: "$.components.schemas.EksComputeConfig.required" + remove: true + + - target: "$.components.schemas.EksComputeConfig" + update: + required: ["region", "clusterName", "workDir"] +``` + +--- + +# Fix Duplicate Enum Values Overlay + +## fix-duplicate-enums-overlay-1.102.0.yaml + +**CRITICAL**: This overlay fixes duplicate enum values in query parameters and schemas using the "remove first, then update" pattern. + +```yaml +overlay: 1.0.0 +info: + title: Fix duplicate enum values overlay + version: 1.102.0 +actions: + # ===== FIX DUPLICATE ENUM VALUES ===== + + # These duplicate enum values exist in the base decorated spec + # We use the "remove first, then update" pattern to fix them + + # ---- Query Parameter: Status (line 563) ---- + + - target: "$.paths./compute-envs.get.parameters[?(@.name=='status')].schema.enum" + remove: true + + - target: "$.paths./compute-envs.get.parameters[?(@.name=='status')].schema" + update: + enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID"] + + # ---- Query Parameter: Attributes (line 809) ---- + + - target: "$.paths./compute-envs/{computeEnvId}.get.parameters[?(@.name=='attributes')].schema.items.enum" + remove: true + + - target: "$.paths./compute-envs/{computeEnvId}.get.parameters[?(@.name=='attributes')].schema.items" + update: + enum: ["labels"] + + # ---- AzBatchConfig.deleteJobsOnCompletion (line 8891) ---- + + - target: "$.components.schemas.AzBatchConfig.properties.deleteJobsOnCompletion.enum" + remove: true + + - target: "$.components.schemas.AzBatchConfig.properties.deleteJobsOnCompletion" + update: + enum: ["on_success", "always", "never"] + + # ---- ComputeEnv_ComputeConfig_.platform (lines 9283-9331) ---- + # This has extensive triplication of values + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.platform.enum" + remove: true + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.platform" + update: + enum: + - "aws-batch" + - "aws-cloud" + - "google-batch" + - "google-cloud" + - "azure-batch" + - "azure-cloud" + - "k8s-platform" + - "eks-platform" + - "gke-platform" + - "uge-platform" + - "slurm-platform" + - "lsf-platform" + - "altair-platform" + - "moab-platform" + - "local-platform" + - "seqeracompute-platform" + + # ---- ComputeEnv_ComputeConfig_.status (line 9361) ---- + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.status.enum" + remove: true + + - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.status" + update: + enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID"] + + # ---- K8sComputeConfig.podCleanup (line 11444) ---- + + - target: "$.components.schemas.K8sComputeConfig.properties.podCleanup.enum" + remove: true + + - target: "$.components.schemas.K8sComputeConfig.properties.podCleanup" + update: + enum: ["on_success", "always", "never"] +``` + +--- + +# Remove Google Life Sciences Platform + +## remove-google-lifesciences-overlay-1.102.0.yaml + +**CRITICAL**: This overlay removes the deprecated google-lifesciences platform option from the API spec entirely. + +```yaml +overlay: 1.0.0 +info: + title: Remove Google Life Sciences platform overlay + version: 1.102.0 +actions: + # ===== REMOVE GOOGLE LIFE SCIENCES PLATFORM ===== + + # This platform option is deprecated and should be removed from the API spec + + # ---- Remove from ComputeEnvResponseDto.platform enum (line 9198) ---- + + - target: "$.components.schemas.ComputeEnvResponseDto.properties.platform.enum" + remove: true + + - target: "$.components.schemas.ComputeEnvResponseDto.properties.platform" + update: + enum: + - "aws-batch" + - "aws-cloud" + - "seqeracompute-platform" + - "google-batch" + - "azure-batch" + - "k8s-platform" + - "eks-platform" + - "gke-platform" + - "uge-platform" + - "slurm-platform" + - "lsf-platform" + - "altair-platform" + + # ---- Remove from ComputeConfig discriminator mapping (line 9140) ---- + + - target: "$.components.schemas.ComputeConfig.discriminator.mapping.google-lifesciences" + remove: true + + # ---- Replace ComputeConfig oneOf array without GoogleLifeSciencesConfig ---- + + # CRITICAL: Remove entire oneOf array first to prevent duplicates + - target: "$.components.schemas.ComputeConfig.oneOf" + remove: true + + # Replace with correct array (no GoogleLifeSciencesConfig, no duplicates) + - target: "$.components.schemas.ComputeConfig" + update: + oneOf: + - $ref: "#/components/schemas/AwsBatchConfig" + - $ref: "#/components/schemas/AwsCloudConfig" + - $ref: "#/components/schemas/SeqeraComputeConfig" + - $ref: "#/components/schemas/GoogleBatchConfig" + - $ref: "#/components/schemas/GoogleCloudConfig" + - $ref: "#/components/schemas/AzBatchConfig" + - $ref: "#/components/schemas/AzCloudConfig" + - $ref: "#/components/schemas/LsfComputeConfig" + - $ref: "#/components/schemas/SlurmComputeConfig" + - $ref: "#/components/schemas/K8sComputeConfig" + - $ref: "#/components/schemas/EksComputeConfig" + - $ref: "#/components/schemas/GkeComputeConfig" + - $ref: "#/components/schemas/UnivaComputeConfig" + - $ref: "#/components/schemas/AltairPbsComputeConfig" + - $ref: "#/components/schemas/MoabComputeConfig" + - $ref: "#/components/schemas/LocalComputeConfig" + + # ---- Remove GoogleLifeSciencesConfig schema definition (line 11229+) ---- + + - target: "$.components.schemas.GoogleLifeSciencesConfig" + remove: true +``` + +--- + +# Add Identities Tag Overlay + +## add-identities-tag-overlay-1.102.0.yaml + +```yaml +overlay: 1.0.0 +info: + title: Add identities tag to global tags + version: 1.102.0 +actions: + # ===== ADD MISSING IDENTITIES TAG ===== + + # CRITICAL: Remove entire tags array first to prevent duplicates + - target: "$.tags" + remove: true + + # Replace with complete array including identities tag + - target: "$" + update: + tags: + - name: actions + description: Pipeline actions + - name: avatars + description: Avatars + - name: compute-envs + description: Compute environments + - name: credentials + description: Credentials + - name: data-links + description: Cloud storage directory paths in Data Explorer + - name: datasets + description: Pipeline input datasets (samplesheets) in CSV or TSV format + - name: ga4gh + description: GA4GH workflow execution service runs + - name: identities + description: Managed identities for centralized credential management + - name: labels + description: Labels and resource labels + - name: launch + description: Workflow launch events + - name: orgs + description: Organizations + - name: pipelines + description: Pipelines + - name: pipeline-secrets + description: Pipeline secrets in a user or workspace context + - name: platforms + description: Computing platforms + - name: service-info + description: Seqera Platform API service information + - name: studios + description: Studios and Studio sessions + - name: teams + description: Teams in an organization context + - name: tokens + description: API access tokens + - name: trace + description: Workflow execution traces + - name: users + description: Users + - name: workflows + description: Workflow executions + - name: workspaces + description: Workspaces in an organization context +``` + +--- + +This completes all the overlay files for version 1.102.0. The overlays are organized by controller/feature and follow all the standards exactly as specified in your style guide. From 2d4eea1299d33774bceff04224b546a6af37ab66 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 21 Jan 2026 16:11:08 +0200 Subject: [PATCH 4/4] Delete claude-generated-overlays.md --- .../specs/claude-generated-overlays.md | 1227 ----------------- 1 file changed, 1227 deletions(-) delete mode 100644 platform-api-docs/scripts/specs/claude-generated-overlays.md diff --git a/platform-api-docs/scripts/specs/claude-generated-overlays.md b/platform-api-docs/scripts/specs/claude-generated-overlays.md deleted file mode 100644 index 2afaff260..000000000 --- a/platform-api-docs/scripts/specs/claude-generated-overlays.md +++ /dev/null @@ -1,1227 +0,0 @@ -# Generated Overlays for v1.102.0 - -This file contains all the overlay files generated from the base-1.95-to-1.102.0-changes.yaml comparison overlay, plus manual enrichments for field descriptions. - -**CRITICAL FIXES**: -- `data-links-operations-overlay-1.102.0.yaml` now correctly REMOVES the deprecated `/data-links/{dataLinkId}/download` endpoint -- `data-links-parameters-overlay-1.102.0.yaml` includes parameter array removal actions to prevent duplicate parameters - ---- - -# Missing Schemas (Must Apply First) - -## add-missing-schema-overlay-1.102.0.yaml - -**CRITICAL**: This schema exists in v1.95 base spec but was accidentally excluded from v1.95 decorated spec. Must be added BEFORE other overlays can reference it in ComputeConfig.oneOf array. - -```yaml -overlay: 1.0.0 -info: - title: Add missing LocalComputeConfig schema - version: 1.102.0 -actions: - # ===== ADD MISSING LocalComputeConfig SCHEMA ===== - - # This schema exists in v1.95 base spec but was accidentally excluded from v1.95 decorated spec - # We need to add it before other overlays can reference it - - - target: "$.components.schemas" - update: - LocalComputeConfig: - type: object - title: Local execution configuration - properties: - workDir: - type: string - description: "Compute environment working directory." - preRunScript: - type: string - description: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - postRunScript: - type: string - description: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - environment: - type: array - description: "Array of environment variables for the compute environment." - items: - $ref: "#/components/schemas/ConfigEnvVariable" - nextflowConfig: - type: string - description: "Additional Nextflow configuration content." - discriminator: - type: string - description: "Property to select the compute config platform." - readOnly: true - waveEnabled: - type: boolean - description: "Enable Wave containers support. See [Wave containers](https://docs.seqera.io/platform-cloud/supported_software/wave)." - fusion2Enabled: - type: boolean - description: "Enable Fusion v2 virtual distributed file system. See [Fusion file system](https://docs.seqera.io/platform-cloud/supported_software/fusion)." -``` - ---- - -# Compute Environments Overlays - -## compute-envs-operations-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Compute environments operations overlay - version: 0.0.0 -actions: - # ===== COMPUTE ENVIRONMENTS - OPERATIONS ===== - - # ---- DISABLE COMPUTE ENVIRONMENT ---- - - - target: "$.paths./compute-envs/{computeEnvId}/disable.post.summary" - update: "Disable compute environment" - - - target: "$.paths./compute-envs/{computeEnvId}/disable.post.description" - update: "Disables the compute environment identified by the given `computeEnvId`. A disabled compute environment cannot be used to launch new workflows or Studio sessions. If the compute environment is primary, it will be automatically unset as primary. See [Disable compute environment](https://docs.seqera.io/platform-cloud/compute-envs/overview#disable-compute-environment)" - - # ---- ENABLE COMPUTE ENVIRONMENT ---- - - - target: "$.paths./compute-envs/{computeEnvId}/enable.post.summary" - update: "Enable compute environment" - - - target: "$.paths./compute-envs/{computeEnvId}/enable.post.description" - update: "Enables the compute environment identified by the given `computeEnvId`. An enabled compute environment can be used to launch new workflows and Studio sessions." -``` - -## compute-envs-parameters-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Compute environments parameters overlay - version: 0.0.0 -actions: - # ===== COMPUTE ENVIRONMENTS PARAMETERS - PATH, QUERY, AND REQUEST BODY ===== - - # ---- DISABLE COMPUTE ENVIRONMENT PARAMETERS ---- - - - target: "$.paths./compute-envs/{computeEnvId}/disable.post.parameters[?(@.name=='computeEnvId')].description" - update: "Compute environment string identifier." - - - target: "$.paths./compute-envs/{computeEnvId}/disable.post.parameters[?(@.name=='workspaceId')].description" - update: "Workspace numeric identifier." - - - target: "$.paths./compute-envs/{computeEnvId}/disable.post.requestBody.description" - update: "Compute environment disable request" - - # ---- ENABLE COMPUTE ENVIRONMENT PARAMETERS ---- - - - target: "$.paths./compute-envs/{computeEnvId}/enable.post.parameters[?(@.name=='computeEnvId')].description" - update: "Compute environment string identifier." - - - target: "$.paths./compute-envs/{computeEnvId}/enable.post.parameters[?(@.name=='workspaceId')].description" - update: "Workspace numeric identifier." - - - target: "$.paths./compute-envs/{computeEnvId}/enable.post.requestBody.description" - update: "Compute environment enable request" -``` - -## compute-envs-schemas-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Compute environments schemas overlay - version: 0.0.0 -actions: - # ===== COMPUTE ENVIRONMENTS SCHEMAS - REQUEST/RESPONSE OBJECTS ===== - - # ---- COMPUTE ENVIRONMENT STATUS ENUM ---- - - - target: "$.components.schemas.ComputeEnv.Status" - update: - type: string - enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID", "DISABLED"] - description: "Compute environment status. Accepts `CREATING`, `AVAILABLE`, `ERRORED`, `INVALID`, or `DISABLED`." -``` - ---- - -# Data Links Overlays - -## data-links-operations-overlay-1.102.0.yaml - -```yaml -actions: - # ===== DATA-LINKS - OPERATIONS ===== - - # Update existing operations - - - target: "$.paths./data-links/{dataLinkId}/browse.get.summary" - update: "Explore data-link" - - - target: "$.paths./data-links/{dataLinkId}/browse.get.description" - update: "Retrieves the content of the data-link associated with the given `dataLinkId`." - - - target: "$.paths./data-links/{dataLinkId}/browse/{path}.get.operationId" - update: "ExploreDataLinkWithPath" - - - target: "$.paths./data-links/{dataLinkId}/upload.post.summary" - update: "Generate data-link file upload URL" - - - target: "$.paths./data-links/{dataLinkId}/upload.post.description" - update: "Creates a URL to upload files to the data-link associated with the given `dataLinkId`. For AWS S3 data-links, an additional follow-up request must be sent after your file upload has completed (or encountered an error) to finalize the upload - see the `/upload/finish` endpoint." - - - target: "$.paths./data-links/{dataLinkId}/upload/{dirPath}.post.operationId" - update: "GenerateDataLinkUploadUrlWithPath" - - - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.summary" - update: "Finish data-link file upload" - - - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.description" - update: "Finish upload of a data-link file. This is necessary for AWS S3 data-links (`DataLinkProvider=aws`) to finalize a successful file upload, or abort an upload if an error was encountered while uploading a file using an upload URL from the `/upload` endpoint." - - - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.responses['404'].description" - update: "NotFound — workspace or credentials not found, API disabled for the workspace, or data-link not found." - - - target: "$.paths./data-links/{dataLinkId}/upload/finish/{dirPath}.post.operationId" - update: "FinishDataLinkUploadWithPath" - - - target: "$.paths./data-links/{dataLinkId}/upload/finish/{dirPath}.post.responses['200'].description" - update: "FinishDataLinkUploadWithPath 200 response." - - # New endpoint in v1.102.0 - - - target: "$.paths" - update: - /data-links/{dataLinkId}/download/{filePath}: - get: - tags: - - data-links - summary: "Download data-link file at path" - description: "Downloads the content at the given `filePath` in the data-link associated with the given `dataLinkId`." - operationId: DownloadDataLink - parameters: - - name: dataLinkId - in: path - description: "Data-link string identifier." - required: true - schema: - type: string - - name: filePath - in: path - description: "Resource path of the file to download." - required: true - schema: - type: string - - name: credentialsId - in: query - description: "Credentials string identifier." - schema: - type: string - - name: workspaceId - in: query - description: "Workspace numeric identifier." - schema: - type: integer - format: int64 - responses: - "200": - description: "OK." - content: - application/json: - schema: - type: string - format: binary - "400": - description: "Bad request." - content: - application/json: - schema: - $ref: "#/components/schemas/ErrorResponse" - "404": - description: "NotFound — workspace or credentials not found, API disabled for the workspace, or data-link or path not found." - content: - application/json: - schema: - $ref: "#/components/schemas/ErrorResponse" - "403": - description: "Operation not allowed." - security: - - BearerAuth: [] - - # Remove deprecated endpoint - - - target: "$.paths./data-links/{dataLinkId}/download" - remove: true -``` - -## data-links-parameters-overlay-1.102.0.yaml - -**CRITICAL**: This overlay includes parameter array removal actions to prevent duplicate parameters. - -```yaml -overlay: 1.0.0 -info: - title: Data-links parameters overlay - version: 1.102.0 -actions: - # ===== DATA-LINKS PARAMETERS ===== - - # ---- /data-links/{dataLinkId}/browse GET ---- - - # CRITICAL: Remove entire parameters array to prevent duplicates - - target: "$.paths./data-links/{dataLinkId}/browse.get.parameters[*]" - remove: true - - # Replace with complete array with enriched descriptions - - target: "$.paths./data-links/{dataLinkId}/browse.get.parameters" - update: - - name: dataLinkId - in: path - description: "Data-link string identifier." - required: true - schema: - type: string - - name: workspaceId - in: query - description: "Workspace numeric identifier." - schema: - type: integer - format: int64 - - name: credentialsId - in: query - description: "Credentials string identifier." - schema: - type: string - - name: search - in: query - description: "Prefix search of data-link content." - schema: - type: string - - name: nextPageToken - in: query - description: "Token used to fetch the next page of items." - schema: - type: string - - name: pageSize - in: query - description: "Number of items to return per page. If omitted, a default maximum value is returned." - schema: - type: integer - format: int32 - - # ---- /data-links/{dataLinkId}/upload POST ---- - - # CRITICAL: Remove entire parameters array to prevent duplicates - - target: "$.paths./data-links/{dataLinkId}/upload.post.parameters[*]" - remove: true - - # Replace with complete array with enriched descriptions - - target: "$.paths./data-links/{dataLinkId}/upload.post.parameters" - update: - - name: dataLinkId - in: path - description: "Data-link string identifier." - required: true - schema: - type: string - - name: credentialsId - in: query - description: "Credentials string identifier." - schema: - type: string - - name: workspaceId - in: query - description: "Workspace numeric identifier." - schema: - type: integer - format: int64 - - name: Origin - in: header - schema: - type: string - nullable: true - - # ---- /data-links/{dataLinkId}/upload/finish POST ---- - - # CRITICAL: Remove entire parameters array to prevent duplicates - - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.parameters[*]" - remove: true - - # Replace with complete array with enriched descriptions - - target: "$.paths./data-links/{dataLinkId}/upload/finish.post.parameters" - update: - - name: dataLinkId - in: path - description: "Data-link string identifier." - required: true - schema: - type: string - - name: credentialsId - in: query - description: "Credentials string identifier." - schema: - type: string - - name: workspaceId - in: query - description: "Workspace numeric identifier." - schema: - type: integer - format: int64 -``` - ---- - -# Workflows Overlays - -## workflows-parameters-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Workflows parameters overlay - version: 0.0.0 -actions: - # ===== WORKFLOWS PARAMETERS - QUERY PARAMETERS ===== - - # ---- LIST WORKFLOWS PARAMETERS ---- - - - target: "$.paths./workflow.get.parameters[?(@.name=='includeTotalSize')].description" - update: "If true, includes total result count in the response. Default: `false`." -``` - -## workflows-operations-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Workflows operations overlay - version: 0.0.0 -actions: - # ===== WORKFLOWS - OPERATIONS ===== - - # ---- LAUNCH WORKFLOW ---- - - - target: "$.paths./workflow/launch.post.description" - update: | - Submits a workflow execution. - - **To [resume](https://docs.seqera.io/platform-cloud/launch/cache-resume#resume-a-workflow-run) a workflow**: First, retrieve the launch configuration using [`GET /workflow/{workflowId}/launch`](https://docs.seqera.io/platform-api/describe-workflow-launch). Then modify the response by setting `workDir` to the value from `resumeDir`, `revision` to the value from `resumeCommitId`, and `resume` to `true`. Submit the modified payload to this endpoint to resume the workflow. -``` - ---- - -# Global Schemas Overlay - -## global-schemas-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Global schemas overlay - version: 0.0.0 -actions: - # ===== GLOBAL SCHEMAS - CREDENTIALS AND COMPUTE CONFIGURATIONS ===== - - # ---- GIT CREDENTIALS ---- - - - target: "$.components.schemas.GitKeys.description" - update: "Git repository credentials." - - - target: "$.components.schemas.GitKeys.properties.discriminator.description" - update: "Property to select the credentials type." - - - target: "$.components.schemas.GitKeys.properties.username.description" - update: "Git username for authentication." - - - target: "$.components.schemas.GitKeys.properties.password.description" - update: "Git password for authentication." - - - target: "$.components.schemas.GitKeys.properties.token.description" - update: "Git personal access token for authentication." - - # ---- SEQERA COMPUTE CLOUD INSTANCE TYPE SIZE ---- - - - target: "$.components.schemas.SeqeraComputeCloudInstanceTypeSize.description" - update: "Data Studios instance size. Accepts `SMALL`, `MEDIUM`, or `LARGE`." - - # ---- SEQERA COMPUTE CONFIG ---- - - - target: "$.components.schemas.SeqeraComputeConfig.properties.instanceTypeSize.description" - update: "Size of the Data Studios instance. Accepts `SMALL`, `MEDIUM`, or `LARGE`." - - # ---- ABSTRACT GRID CONFIG ---- - - - target: "$.components.schemas.AbstractGridConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.AbstractGridConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.AbstractGridConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.AbstractGridConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.AbstractGridConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.AbstractGridConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.AbstractGridConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.AbstractGridConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.AbstractGridConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.AbstractGridConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.AbstractGridConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.AbstractGridConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.AbstractGridConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.AbstractGridConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.AbstractGridConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - # ---- LSF COMPUTE CONFIG ---- - - - target: "$.components.schemas.LsfComputeConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.LsfComputeConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.LsfComputeConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.LsfComputeConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.LsfComputeConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.LsfComputeConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.LsfComputeConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.LsfComputeConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.LsfComputeConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.LsfComputeConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.LsfComputeConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.LsfComputeConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.LsfComputeConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.LsfComputeConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.LsfComputeConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - - target: "$.components.schemas.LsfComputeConfig.properties.unitForLimits.description" - update: "Unit for memory and time limits in LSF." - - - target: "$.components.schemas.LsfComputeConfig.properties.perJobMemLimit.description" - update: "If true, applies memory limit per job. Default: `false`." - - - target: "$.components.schemas.LsfComputeConfig.properties.perTaskReserve.description" - update: "If true, reserves resources per task. Default: `false`." - - # ---- SLURM COMPUTE CONFIG ---- - - - target: "$.components.schemas.SlurmComputeConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.SlurmComputeConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.SlurmComputeConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.SlurmComputeConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.SlurmComputeConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.SlurmComputeConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.SlurmComputeConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.SlurmComputeConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.SlurmComputeConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.SlurmComputeConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.SlurmComputeConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.SlurmComputeConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.SlurmComputeConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.SlurmComputeConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.SlurmComputeConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - # ---- ALTAIR PBS COMPUTE CONFIG ---- - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.AltairPbsComputeConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - # ---- MOAB COMPUTE CONFIG ---- - - - target: "$.components.schemas.MoabComputeConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.MoabComputeConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.MoabComputeConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.MoabComputeConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.MoabComputeConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.MoabComputeConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.MoabComputeConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.MoabComputeConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.MoabComputeConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.MoabComputeConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.MoabComputeConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.MoabComputeConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.MoabComputeConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.MoabComputeConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.MoabComputeConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - # ---- UNIVA COMPUTE CONFIG ---- - - - target: "$.components.schemas.UnivaComputeConfig.properties.workDir.description" - update: "Compute environment working directory." - - - target: "$.components.schemas.UnivaComputeConfig.properties.preRunScript.description" - update: "Script that executes in the nf-launch script prior to invoking Nextflow processes. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.UnivaComputeConfig.properties.postRunScript.description" - update: "Script that executes after all Nextflow processes have completed. See [Pre and post-run scripts](https://docs.seqera.io/platform-cloud/launch/advanced#pre-and-post-run-scripts)." - - - target: "$.components.schemas.UnivaComputeConfig.properties.environment.description" - update: "Array of environment variables for the compute environment." - - - target: "$.components.schemas.UnivaComputeConfig.properties.nextflowConfig.description" - update: "Additional Nextflow configuration content." - - - target: "$.components.schemas.UnivaComputeConfig.properties.discriminator.description" - update: "Property to select the compute config platform." - - - target: "$.components.schemas.UnivaComputeConfig.properties.launchDir.description" - update: "Launch directory for Nextflow execution." - - - target: "$.components.schemas.UnivaComputeConfig.properties.userName.description" - update: "Username for SSH authentication to the HPC cluster." - - - target: "$.components.schemas.UnivaComputeConfig.properties.hostName.description" - update: "Hostname or IP address of the HPC cluster head node." - - - target: "$.components.schemas.UnivaComputeConfig.properties.port.description" - update: "SSH port for connecting to the HPC cluster. Default: `22`." - - - target: "$.components.schemas.UnivaComputeConfig.properties.headQueue.description" - update: "Queue name for submitting the Nextflow head job." - - - target: "$.components.schemas.UnivaComputeConfig.properties.computeQueue.description" - update: "Queue name for submitting Nextflow compute jobs." - - - target: "$.components.schemas.UnivaComputeConfig.properties.maxQueueSize.description" - update: "Maximum number of jobs that can be queued at one time." - - - target: "$.components.schemas.UnivaComputeConfig.properties.headJobOptions.description" - update: "Additional options for the head job submission." - - - target: "$.components.schemas.UnivaComputeConfig.properties.propagateHeadJobOptions.description" - update: "If true, head job options are propagated to compute jobs. Default: `false`." - - # ---- EKS COMPUTE CONFIG ---- - - - target: "$.components.schemas.EksComputeConfig.properties.region.description" - update: "AWS region where the EKS cluster is located." - - - target: "$.components.schemas.EksComputeConfig.properties.clusterName.description" - update: "Name of the AWS EKS cluster." - - # ---- GKE COMPUTE CONFIG ---- - - - target: "$.components.schemas.GkeComputeConfig.properties.region.description" - update: "Google Cloud region or zone where the GKE cluster is located." - - - target: "$.components.schemas.GkeComputeConfig.properties.clusterName.description" - update: "Name of the Google GKE cluster." - - # ---- WORKFLOW AND TASK SCHEMAS ---- - - - target: "$.components.schemas.Task.properties.numSpotInterruptions.description" - update: "Number of spot instance interruptions encountered by this task." - - - target: "$.components.schemas.TraceProgressData.properties.numSpotInterruptions.description" - update: "Total number of spot instance interruptions across all tasks." - - - target: "$.components.schemas.WorkflowLoad.properties.numSpotInterruptions.description" - update: "Number of spot instance interruptions for the workflow." - - # ---- LIST WORKFLOWS RESPONSE ---- - - - target: "$.components.schemas.ListWorkflowsResponse.properties.hasMore.description" - update: "If true, indicates there are more results available beyond this page." - - # ---- ORGANIZATION QUOTAS ---- - - - target: "$.components.schemas.OrganizationQuotas.properties.maxCustomRolesPerOrg.description" - update: "Maximum number of custom roles allowed per organization." - - # ---- DATA STUDIO STOP REASON ---- - - - target: "$.components.schemas.DataStudioStopReason.description" - update: "Reason for Data Studio session termination. Accepts `UNKNOWN`, `USER_REQUEST`, `TIMEOUT`, `ERROR`, `RESOURCE_LIMIT`, or `NO_STATS_AVAIL`." -``` - ---- - -# Manual Field Descriptions Overlay - -## manual-field-descriptions-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Manual field descriptions overlay - version: 0.0.0 -actions: - # ===== PIPELINE SECRETS SCHEMAS ===== - - # ---- CREATE PIPELINE SECRET REQUEST ---- - - - target: "$.components.schemas.CreatePipelineSecretRequest.properties.name.description" - update: "Unique name for the pipeline secret within the workspace. Used to reference the secret in workflow configurations." - - - target: "$.components.schemas.CreatePipelineSecretRequest.properties.value.description" - update: "The secret value to be securely stored. This value will be made available to pipeline executions as an environment variable or configuration value." - - # ---- UPDATE PIPELINE SECRET REQUEST ---- - - - target: "$.components.schemas.UpdatePipelineSecretRequest.properties.value.description" - update: "New secret value to replace the existing value. The secret value is securely stored and made available to pipeline executions." - - # ===== DATASETS SCHEMAS ===== - - # ---- CREATE DATASET REQUEST ---- - - - target: "$.components.schemas.CreateDatasetRequest.properties.name.description" - update: "Unique dataset name within the workspace. Must be a valid identifier that can be referenced in workflow configurations." - - - target: "$.components.schemas.CreateDatasetRequest.properties.description.description" - update: "Optional description of the dataset. Provides context about the dataset contents, source, or intended use." - - # ---- UPDATE DATASET REQUEST ---- - - - target: "$.components.schemas.UpdateDatasetRequest.properties.name.description" - update: "New name for the dataset. Must be unique within the workspace and can be used to reference the dataset in workflow configurations." - - - target: "$.components.schemas.UpdateDatasetRequest.properties.description.description" - update: "Updated description for the dataset. Provides context about the dataset contents, source, or intended use." - - # ===== WORKSPACES SCHEMAS ===== - - # ---- UPDATE WORKSPACE REQUEST ---- - - - target: "$.components.schemas.UpdateWorkspaceRequest.properties.name.description" - update: "New short name for the workspace. Must be 2-40 characters, start and end with alphanumeric characters, and can contain hyphens or underscores between characters. Must be unique within the organization." - - - target: "$.components.schemas.UpdateWorkspaceRequest.properties.fullName.description" - update: "Updated full display name for the workspace. Maximum 100 characters." - - - target: "$.components.schemas.UpdateWorkspaceRequest.properties.description.description" - update: "Updated description of the workspace. Maximum 1000 characters." - - # ===== ACTIONS SCHEMAS ===== - - # ---- UPDATE ACTION REQUEST ---- - - - target: "$.components.schemas.UpdateActionRequest.properties.name.description" - update: "New name for the pipeline action. Must be unique within the workspace." -``` - ---- - -# Fix Duplicate Required Fields Overlay - -## fix-duplicate-required-fields-overlay-1.102.0.yaml - -**CRITICAL**: This overlay fixes duplicate required fields in compute config schemas using the "remove first, then update" pattern. - -```yaml -overlay: 1.0.0 -info: - title: Fix duplicate required fields overlay - version: 1.102.0 -actions: - # ===== FIX DUPLICATE REQUIRED FIELDS ===== - - # These duplicate required fields exist in the base spec - # We use the "remove first, then update" pattern to fix them - - # ---- AwsBatchConfig ---- - - - target: "$.components.schemas.AwsBatchConfig.required" - remove: true - - - target: "$.components.schemas.AwsBatchConfig" - update: - required: ["region", "workDir"] - - # ---- AwsCloudConfig ---- - - - target: "$.components.schemas.AwsCloudConfig.required" - remove: true - - - target: "$.components.schemas.AwsCloudConfig" - update: - required: ["region", "workDir"] - - # ---- AzBatchConfig ---- - - - target: "$.components.schemas.AzBatchConfig.required" - remove: true - - - target: "$.components.schemas.AzBatchConfig" - update: - required: ["region", "workDir"] - - # ---- AzCloudConfig ---- - - - target: "$.components.schemas.AzCloudConfig.required" - remove: true - - - target: "$.components.schemas.AzCloudConfig" - update: - required: ["location", "workDir"] - - # ---- ConfigEnvVariable ---- - - - target: "$.components.schemas.ConfigEnvVariable.required" - remove: true - - - target: "$.components.schemas.ConfigEnvVariable" - update: - required: ["name", "value"] - - # ---- CreateComputeEnvRequest ---- - - - target: "$.components.schemas.CreateComputeEnvRequest.required" - remove: true - - - target: "$.components.schemas.CreateComputeEnvRequest" - update: - required: ["computeEnv"] - - # ---- GkeComputeConfig ---- - - - target: "$.components.schemas.GkeComputeConfig.required" - remove: true - - - target: "$.components.schemas.GkeComputeConfig" - update: - required: ["region", "clusterName", "workDir"] - - # ---- GoogleBatchConfig ---- - - - target: "$.components.schemas.GoogleBatchConfig.required" - remove: true - - - target: "$.components.schemas.GoogleBatchConfig" - update: - required: ["location", "workDir"] - - # ---- GoogleCloudConfig ---- - - - target: "$.components.schemas.GoogleCloudConfig.required" - remove: true - - - target: "$.components.schemas.GoogleCloudConfig" - update: - required: ["region", "workDir"] - - # ---- K8sComputeConfig ---- - - - target: "$.components.schemas.K8sComputeConfig.required" - remove: true - - - target: "$.components.schemas.K8sComputeConfig" - update: - required: ["server", "sslCert", "workDir"] - - # ---- SeqeraComputeConfig ---- - - - target: "$.components.schemas.SeqeraComputeConfig.required" - remove: true - - - target: "$.components.schemas.SeqeraComputeConfig" - update: - required: ["region", "workDir"] - - # ---- ComputeEnv_ComputeConfig_ ---- - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_.required" - remove: true - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_" - update: - required: ["config", "name", "platform"] - - # ---- EksComputeConfig ---- - - - target: "$.components.schemas.EksComputeConfig.required" - remove: true - - - target: "$.components.schemas.EksComputeConfig" - update: - required: ["region", "clusterName", "workDir"] -``` - ---- - -# Fix Duplicate Enum Values Overlay - -## fix-duplicate-enums-overlay-1.102.0.yaml - -**CRITICAL**: This overlay fixes duplicate enum values in query parameters and schemas using the "remove first, then update" pattern. - -```yaml -overlay: 1.0.0 -info: - title: Fix duplicate enum values overlay - version: 1.102.0 -actions: - # ===== FIX DUPLICATE ENUM VALUES ===== - - # These duplicate enum values exist in the base decorated spec - # We use the "remove first, then update" pattern to fix them - - # ---- Query Parameter: Status (line 563) ---- - - - target: "$.paths./compute-envs.get.parameters[?(@.name=='status')].schema.enum" - remove: true - - - target: "$.paths./compute-envs.get.parameters[?(@.name=='status')].schema" - update: - enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID"] - - # ---- Query Parameter: Attributes (line 809) ---- - - - target: "$.paths./compute-envs/{computeEnvId}.get.parameters[?(@.name=='attributes')].schema.items.enum" - remove: true - - - target: "$.paths./compute-envs/{computeEnvId}.get.parameters[?(@.name=='attributes')].schema.items" - update: - enum: ["labels"] - - # ---- AzBatchConfig.deleteJobsOnCompletion (line 8891) ---- - - - target: "$.components.schemas.AzBatchConfig.properties.deleteJobsOnCompletion.enum" - remove: true - - - target: "$.components.schemas.AzBatchConfig.properties.deleteJobsOnCompletion" - update: - enum: ["on_success", "always", "never"] - - # ---- ComputeEnv_ComputeConfig_.platform (lines 9283-9331) ---- - # This has extensive triplication of values - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.platform.enum" - remove: true - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.platform" - update: - enum: - - "aws-batch" - - "aws-cloud" - - "google-batch" - - "google-cloud" - - "azure-batch" - - "azure-cloud" - - "k8s-platform" - - "eks-platform" - - "gke-platform" - - "uge-platform" - - "slurm-platform" - - "lsf-platform" - - "altair-platform" - - "moab-platform" - - "local-platform" - - "seqeracompute-platform" - - # ---- ComputeEnv_ComputeConfig_.status (line 9361) ---- - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.status.enum" - remove: true - - - target: "$.components.schemas.ComputeEnv_ComputeConfig_.properties.status" - update: - enum: ["CREATING", "AVAILABLE", "ERRORED", "INVALID"] - - # ---- K8sComputeConfig.podCleanup (line 11444) ---- - - - target: "$.components.schemas.K8sComputeConfig.properties.podCleanup.enum" - remove: true - - - target: "$.components.schemas.K8sComputeConfig.properties.podCleanup" - update: - enum: ["on_success", "always", "never"] -``` - ---- - -# Remove Google Life Sciences Platform - -## remove-google-lifesciences-overlay-1.102.0.yaml - -**CRITICAL**: This overlay removes the deprecated google-lifesciences platform option from the API spec entirely. - -```yaml -overlay: 1.0.0 -info: - title: Remove Google Life Sciences platform overlay - version: 1.102.0 -actions: - # ===== REMOVE GOOGLE LIFE SCIENCES PLATFORM ===== - - # This platform option is deprecated and should be removed from the API spec - - # ---- Remove from ComputeEnvResponseDto.platform enum (line 9198) ---- - - - target: "$.components.schemas.ComputeEnvResponseDto.properties.platform.enum" - remove: true - - - target: "$.components.schemas.ComputeEnvResponseDto.properties.platform" - update: - enum: - - "aws-batch" - - "aws-cloud" - - "seqeracompute-platform" - - "google-batch" - - "azure-batch" - - "k8s-platform" - - "eks-platform" - - "gke-platform" - - "uge-platform" - - "slurm-platform" - - "lsf-platform" - - "altair-platform" - - # ---- Remove from ComputeConfig discriminator mapping (line 9140) ---- - - - target: "$.components.schemas.ComputeConfig.discriminator.mapping.google-lifesciences" - remove: true - - # ---- Replace ComputeConfig oneOf array without GoogleLifeSciencesConfig ---- - - # CRITICAL: Remove entire oneOf array first to prevent duplicates - - target: "$.components.schemas.ComputeConfig.oneOf" - remove: true - - # Replace with correct array (no GoogleLifeSciencesConfig, no duplicates) - - target: "$.components.schemas.ComputeConfig" - update: - oneOf: - - $ref: "#/components/schemas/AwsBatchConfig" - - $ref: "#/components/schemas/AwsCloudConfig" - - $ref: "#/components/schemas/SeqeraComputeConfig" - - $ref: "#/components/schemas/GoogleBatchConfig" - - $ref: "#/components/schemas/GoogleCloudConfig" - - $ref: "#/components/schemas/AzBatchConfig" - - $ref: "#/components/schemas/AzCloudConfig" - - $ref: "#/components/schemas/LsfComputeConfig" - - $ref: "#/components/schemas/SlurmComputeConfig" - - $ref: "#/components/schemas/K8sComputeConfig" - - $ref: "#/components/schemas/EksComputeConfig" - - $ref: "#/components/schemas/GkeComputeConfig" - - $ref: "#/components/schemas/UnivaComputeConfig" - - $ref: "#/components/schemas/AltairPbsComputeConfig" - - $ref: "#/components/schemas/MoabComputeConfig" - - $ref: "#/components/schemas/LocalComputeConfig" - - # ---- Remove GoogleLifeSciencesConfig schema definition (line 11229+) ---- - - - target: "$.components.schemas.GoogleLifeSciencesConfig" - remove: true -``` - ---- - -# Add Identities Tag Overlay - -## add-identities-tag-overlay-1.102.0.yaml - -```yaml -overlay: 1.0.0 -info: - title: Add identities tag to global tags - version: 1.102.0 -actions: - # ===== ADD MISSING IDENTITIES TAG ===== - - # CRITICAL: Remove entire tags array first to prevent duplicates - - target: "$.tags" - remove: true - - # Replace with complete array including identities tag - - target: "$" - update: - tags: - - name: actions - description: Pipeline actions - - name: avatars - description: Avatars - - name: compute-envs - description: Compute environments - - name: credentials - description: Credentials - - name: data-links - description: Cloud storage directory paths in Data Explorer - - name: datasets - description: Pipeline input datasets (samplesheets) in CSV or TSV format - - name: ga4gh - description: GA4GH workflow execution service runs - - name: identities - description: Managed identities for centralized credential management - - name: labels - description: Labels and resource labels - - name: launch - description: Workflow launch events - - name: orgs - description: Organizations - - name: pipelines - description: Pipelines - - name: pipeline-secrets - description: Pipeline secrets in a user or workspace context - - name: platforms - description: Computing platforms - - name: service-info - description: Seqera Platform API service information - - name: studios - description: Studios and Studio sessions - - name: teams - description: Teams in an organization context - - name: tokens - description: API access tokens - - name: trace - description: Workflow execution traces - - name: users - description: Users - - name: workflows - description: Workflow executions - - name: workspaces - description: Workspaces in an organization context -``` - ---- - -This completes all the overlay files for version 1.102.0. The overlays are organized by controller/feature and follow all the standards exactly as specified in your style guide.