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Merge pull request #207 from seqeralabs/improved-ia
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Platform docs IA update
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@llewellyn-sl
llewellyn-sl authored Sep 6, 2024
2 parents a5538a9 + 05654f1 commit 847ca39
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278 changes: 136 additions & 142 deletions platform_versioned_docs/version-23.4/enterprise/general_troubleshooting.mdx
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2 changes: 1 addition & 1 deletion platform_versioned_docs/version-23.4/faqs.mdx
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---
title: "FAQ and troubleshooting"
title: "FAQ"
description: "Frequently asked questions and troubleshooting."
date: "24 Apr 2023"
tags: [faq, help]
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4 changes: 2 additions & 2 deletions platform_versioned_docs/version-23.4/functionality_matrix/functionality_matrix.mdx
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---
title: "Platform / Nextflow base versions"
description: "Platform / nf-launcher / Nextflow base versions"
title: "Version compatibility"
description: "Platform / nf-launcher / Nextflow / Fusion version compatibility"
date: "21 Apr 2023"
tags: [compatibility, nextflow, nf-launcher]
---
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12 changes: 2 additions & 10 deletions platform_versioned_docs/version-23.4/launch/launchpad.mdx
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Expand Up @@ -51,21 +51,16 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu
1. On the **Launch** form, enter an optional **Workflow run name** (or keep the randomly assigned default) and assign optional labels to the run.
1. Select a **Compute environment** from the available options. See [Compute environments](../compute-envs/overview.mdx) to learn how to create an environment for your preferred execution platform.
1. Enter a repository URL for the **Pipeline to launch** (e.g., `https://github.com/nf-core/rnaseq.git`).

:::note
Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See [Git integration](../git/overview.mdx) in the Seqera docs and [Pipeline sharing](https://www.nextflow.io/docs/latest/sharing.html) in the Nextflow docs for more details.
:::

1. Select a **Revision number** to use a specific version of the pipeline (optional). The Git default branch (e.g. main or master) or `manifest.defaultBranch` in the Nextflow configuration will be used by default.
1. Enter the **Work directory**, which corresponds to the Nextflow work directory. You can also **Browse** for a cloud storage directory with Data Explorer. The default work directory of the compute environment will be used by default.

:::note
The credentials associated with the compute environment must have access to the work directory (e.g., an S3 bucket).
:::

1. Select any **Config profiles** you wish to use. See [Nextflow Config profiles](https://www.nextflow.io/docs/latest/config.html#config-profiles) for more details.
1. Enter any **Pipeline parameters** in YAML or JSON format:

```
reads: 's3://nf-bucket/exome-data/ERR013140_{1,2}.fastq.bz2'
paired_end: true
Expand All @@ -74,14 +69,9 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu
:::note
In YAML, quotes should be used for paths but not for numbers or Boolean values.
:::


1. Select or create [resource labels](../resource-labels/overview.mdx) to apply to the resources consumed by the run, if needed.

1. Expand the [Pipeline secrets](../secrets/overview.mdx) dropdown to select user or workspace secrets to be used during the run, if needed.

1. Apply any [Advanced options](./advanced.mdx), if needed.

1. When you have filled the necessary launch form details, select **Launch**. The **Runs** tab shows your new run in a **submitted** status on the top of the list. Select the run name to navigate to the run detail page and view the configuration, parameters, status of individual tasks, and run report.

:::note
Expand All @@ -92,6 +82,8 @@ For more information on relaunch and resume, see [Cache and resume](./cache-resu

From the Launchpad, select **Add pipeline** to add a new pipeline with pre-saved parameters to your workspace. The fields on the new pipeline form are similar to the pipeline launch form.

See [Add pipelines](../getting-started/quickstart-demo/add-pipelines.mdx) for instructions to add pipelines to your workspace via [Seqera Pipelines](https://seqera.io/pipelines) or the Launchpad.

:::tip
To create your own customized Nextflow schema for your pipeline, see [Pipeline schema](../pipeline-schema/overview.mdx) and the `nf-core` workflows that have adopted this. [nf-core/eager](https://github.com/nf-core/eager/blob/2.3.3/nextflow_schema.json) and [nf-core/rnaseq](https://github.com/nf-core/rnaseq/blob/3.0/nextflow_schema.json) are excellent examples.
:::
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278 changes: 136 additions & 142 deletions platform_versioned_docs/version-24.1/enterprise/general_troubleshooting.mdx
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2 changes: 1 addition & 1 deletion platform_versioned_docs/version-24.1/faqs.mdx
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---
title: "FAQ and troubleshooting"
title: "FAQ"
description: "Frequently asked questions and troubleshooting."
date: "24 Apr 2023"
tags: [faq, help]
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4 changes: 2 additions & 2 deletions platform_versioned_docs/version-24.1/functionality_matrix/functionality_matrix.mdx
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---
title: "Platform / Nextflow base versions"
description: "Platform / nf-launcher / Nextflow base versions"
title: "Version compatibility"
description: "Platform / nf-launcher / Nextflow / Fusion version compatibility"
date: "20 Jun 2024"
tags: [compatibility, nextflow, nf-launcher]
---
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2 changes: 2 additions & 0 deletions platform_versioned_docs/version-24.1/launch/launchpad.mdx
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Expand Up @@ -91,6 +91,8 @@ For more information on relaunch and resume, see [Nextflow cache and resume](./c

From the **Launchpad**, select **Add pipeline** to add a new pipeline with pre-saved parameters to your workspace. The fields on the new pipeline form are similar to the pipeline launch form.

See [Add pipelines](../getting-started/quickstart-demo/add-pipelines.mdx) for instructions to add pipelines to your workspace via [Seqera Pipelines](https://seqera.io/pipelines) or the Launchpad.

:::note
Pipeline names must be unique per workspace.
:::
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220 changes: 104 additions & 116 deletions platform_versioned_sidebars/version-23.4-sidebars.json
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{
"platformSidebar": [
"index",
{
"type": "category",
"label": "Tutorials",
"collapsed": true,
"items": [
"getting-started/quickstart-demo/comm-showcase"
]
},
{
"type": "category",
"label": "Get started",
"collapsed": false,
"collapsed": true,
"items": [
"getting-started/quickstart-demo/comm-showcase",
"getting-started/deployment-options",
"getting-started/workspace-setup",
"getting-started/quickstart-demo/add-pipelines",
"getting-started/quickstart-demo/add-data",
"getting-started/quickstart-demo/launch-pipelines",
"getting-started/quickstart-demo/monitor-runs",
"getting-started/quickstart-demo/automation"
"getting-started/quickstart-demo/automation"
]
},
},
{
"type": "category",
"label": "User guide",
"collapsed": true,
"label": "Credentials",
"items": [
"credentials/overview",
"git/overview",
{
"type": "category",
"label": "Administration",
"items": [
"administration/overview",
"orgs-and-teams/organizations",
"orgs-and-teams/workspace-management",
"orgs-and-teams/roles"
]
},
{
"type": "category",
"label": "Credentials",
"label": "Container registry credentials",
"items": [
"credentials/overview",
"git/overview",
{
"type": "category",
"label": "Container registry credentials",
"items": [
"credentials/docker_hub_registry_credentials",
"credentials/aws_registry_credentials",
"credentials/azure_registry_credentials",
"credentials/google_registry_credentials",
"credentials/quay_registry_credentials",
"credentials/gitlab_registry_credentials",
"credentials/github_registry_credentials",
"credentials/gitea_registry_credentials"
]
},
"credentials/ssh_credentials",
"credentials/agent_credentials"
"credentials/docker_hub_registry_credentials",
"credentials/aws_registry_credentials",
"credentials/azure_registry_credentials",
"credentials/google_registry_credentials",
"credentials/quay_registry_credentials",
"credentials/gitlab_registry_credentials",
"credentials/github_registry_credentials",
"credentials/gitea_registry_credentials"
]
},
"credentials/ssh_credentials",
"credentials/agent_credentials"
]
},
{
"type": "category",
"label": "Compute",
"items": [
"compute-envs/overview",
{
"type": "category",
"label": "Data",
"label": "Cloud",
"items": [
"data/data-explorer",
"data/data-studios",
"data/datasets"
"compute-envs/aws-batch",
"compute-envs/azure-batch",
"compute-envs/google-cloud-batch",
"compute-envs/google-cloud-lifesciences",
"compute-envs/eks",
"compute-envs/gke"
]
},
"compute-envs/k8s",
"compute-envs/hpc",
"resource-labels/overview",
"supported_software/fusion/fusion",
"supported_software/agent/agent",
"supported_software/dragen/overview",
{
"type": "category",
"label": "Compute",
"items": [
"compute-envs/overview",
{
"type": "category",
"label": "Cloud",
"items": [
"compute-envs/aws-batch",
"compute-envs/azure-batch",
"compute-envs/google-cloud-batch",
"compute-envs/google-cloud-lifesciences",
"compute-envs/eks",
"compute-envs/gke"
]
},
"compute-envs/k8s",
"compute-envs/hpc"
"label": "Advanced options",
"items":[
"enterprise/advanced-topics/manual-aws-batch-setup"
]
},
}
]
},
{
"type": "category",
"label": "Data",
"items": [
"getting-started/quickstart-demo/add-data",
"data/data-explorer",
"data/datasets"
]
},
{
"type": "category",
"label": "Pipelines",
"items": [
"getting-started/quickstart-demo/add-pipelines",
"pipeline-schema/overview",
"launch/launchpad",
"labels/overview",
{
"type": "category",
"label": "Launch",
"items": [
"launch/launchpad",
"launch/cache-resume",
"pipeline-optimization/overview",
"launch/advanced"
]
},
{
"type": "category",
"label": "Monitoring",
"items": [
{
"type": "category",
"label": "Runs",
"items": [
"monitoring/overview",
"monitoring/dashboard",
"monitoring/run-details"
]
},
"monitoring/audit-logs",
"monitoring/cloud-costs"
]
},
{
"type": "category",
"label": "Label",
"items": [
"labels/overview",
"resource-labels/overview"
]
"type": "category",
"label": "Monitor runs",
"items": [
"monitoring/overview",
"monitoring/dashboard",
"monitoring/run-details"
]
},
"secrets/overview",
"pipeline-actions/overview",
"reports/overview",
{
"type": "category",
"label": "Software integration",
"items": [
"supported_software/agent/agent",
"supported_software/fusion/fusion",
"supported_software/dragen/overview"
]
},
{
"type": "category",
"label": "Advanced options",
"items":[
"enterprise/advanced-topics/manual-aws-batch-setup"
]
}
"launch/cache-resume",
"secrets/overview",
"pipeline-optimization/overview",
"launch/advanced"
]
},
{
"type": "category",
"label": "Installation guide",
"label": "Administration",
"items": [
"getting-started/workspace-setup",
"administration/overview",
"orgs-and-teams/organizations",
"orgs-and-teams/workspace-management",
"orgs-and-teams/roles",
"monitoring/audit-logs",
"monitoring/cloud-costs"
]
},
{
"type": "category",
"label": "Enterprise",
"collapsed": true,
"items": [
"enterprise/index",
Expand Down Expand Up @@ -180,27 +164,33 @@
"items": [
"enterprise/docker-compose",
"enterprise/kubernetes",
"enterprise/testing"
"enterprise/testing"
]
},
{
"type": "category",
"label": "Advanced topics",
"label": "Advanced",
"collapsed": true,
"items": [
"enterprise/advanced-topics/db-docker-to-RDS",
"enterprise/advanced-topics/use-iam-role",
"enterprise/advanced-topics/custom-launch-container",
"enterprise/advanced-topics/firewall-configuration"
]
}
},
"enterprise/general_troubleshooting"
]
},
{
"type": "category",
"label": "Developer tools",
"collapsed": true,
"items": [
{
"type": "doc",
"id": "getting-started/quickstart-demo/automation",
"label": "Overview"
},
"api/overview",
{
"type": "category",
Expand Down Expand Up @@ -228,7 +218,7 @@
"label": "Releases",
"collapsed": true,
"items": [
"enterprise/release_notes/changelog",
"enterprise/release_notes/changelog",
"enterprise/release_notes/cloud_latest",
"enterprise/release_notes/enterprise_latest",
{
Expand All @@ -240,9 +230,7 @@
"enterprise/release_notes/23.2",
"enterprise/release_notes/23.1",
"enterprise/release_notes/22.4",
"enterprise/release_notes/22.3",
"enterprise/release_notes/22.2",
"enterprise/release_notes/21.12"
"enterprise/release_notes/22.3"
]
},
"functionality_matrix/functionality_matrix"
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