# Seqera Docs

> Documentation for Seqera products — Seqera Platform Cloud, Seqera Platform Enterprise, Seqera Platform API, Seqera Platform CLI, Nextflow, MultiQC, Fusion, and Wave.

This file contains links to all Seqera product documentation following the llmstxt.org standard.

# Seqera Platform Enterprise

> Documentation for Seqera Platform Enterprise.

This file contains links to Seqera Platform Enterprise documentation following the llmstxt.org standard.

## Table of Contents

- [Admin panel](https://docs.seqera.io//platform-enterprise_docs/administration/overview.md): Overview of Seqera user and organization administration
- [Authentication](https://docs.seqera.io//platform-enterprise_docs/co-scientist/authentication.md): Log in, log out, and manage organizations and tokens in the Seqera CLI
- [Coding agents](https://docs.seqera.io//platform-enterprise_docs/co-scientist/coding-agents.md): Install Co-Scientist as a skill so your coding agent can drive Seqera Platform
- [Command approval](https://docs.seqera.io//platform-enterprise_docs/co-scientist/command-approval.md): Control which local commands require user approval in Co-Scientist
- [Using Co-Scientist](https://docs.seqera.io//platform-enterprise_docs/co-scientist/configuration.md): Use Co-Scientist day to day in the Seqera CLI
- [Co-Scientist in Seqera CLI](https://docs.seqera.io//platform-enterprise_docs/co-scientist/index.md): AI-powered assistant for bioinformatics workflows and Seqera Platform
- [Installation](https://docs.seqera.io//platform-enterprise_docs/co-scientist/installation.md): Install and configure the Seqera CLI
- [Modes](https://docs.seqera.io//platform-enterprise_docs/co-scientist/modes.md): Work in Co-Scientist's build, plan, and goal modes
- [Code intelligence](https://docs.seqera.io//platform-enterprise_docs/co-scientist/nextflow-lsp.md): Use language-server code intelligence in Co-Scientist
- [Prerequisites](https://docs.seqera.io//platform-enterprise_docs/co-scientist/prerequisites.md): Prerequisites for Co-Scientist
- [Projects](https://docs.seqera.io//platform-enterprise_docs/co-scientist/projects.md): Organize workspace resources into projects using Seqera Platform labels
- [Quickstart](https://docs.seqera.io//platform-enterprise_docs/co-scientist/quickstart.md): Run your first Co-Scientist session in the Seqera CLI
- [CLI](https://docs.seqera.io//platform-enterprise_docs/co-scientist/reference/cli.md): Seqera CLI commands and options for Co-Scientist
- [Environment variables](https://docs.seqera.io//platform-enterprise_docs/co-scientist/reference/environment-variables.md): Environment variables for authenticating and configuring the Seqera CLI
- [Reference](https://docs.seqera.io//platform-enterprise_docs/co-scientist/reference/index.md): Reference material for the Seqera CLI and Co-Scientist
- [Skills](https://docs.seqera.io//platform-enterprise_docs/co-scientist/reference/skills-reference.md): Built-in skills, slash commands, and session limits for the Seqera CLI
- [Sessions](https://docs.seqera.io//platform-enterprise_docs/co-scientist/sessions.md): Start, continue, resume, and exit Co-Scientist sessions, and run non-interactively
- [Claude Code](https://docs.seqera.io//platform-enterprise_docs/co-scientist/skill-claude-code.md): Install and maintain the Co-Scientist skill for Claude Code
- [Codex](https://docs.seqera.io//platform-enterprise_docs/co-scientist/skill-codex.md): Install and maintain the Co-Scientist skill for Codex
- [GitHub Copilot](https://docs.seqera.io//platform-enterprise_docs/co-scientist/skill-github-copilot.md): Install and maintain the Co-Scientist skill for GitHub Copilot
- [Other coding agents](https://docs.seqera.io//platform-enterprise_docs/co-scientist/skill-other-agents.md): Install and maintain the Co-Scientist skill for other coding agents
- [Skills configuration](https://docs.seqera.io//platform-enterprise_docs/co-scientist/skills.md): Discover, create, and install skills in the Seqera CLI
- [Usage and cost](https://docs.seqera.io//platform-enterprise_docs/co-scientist/usage-and-cost.md): Understand Co-Scientist usage and inference costs in Seqera Platform Enterprise
- [Use cases](https://docs.seqera.io//platform-enterprise_docs/co-scientist/use-cases.md): Common tasks you can do with Co-Scientist, with example prompts
- [AWS Batch](https://docs.seqera.io//platform-enterprise_docs/compute-envs/aws-batch.md): Instructions to set up AWS Batch in Seqera Platform
- [AWS Cloud](https://docs.seqera.io//platform-enterprise_docs/compute-envs/aws-cloud.md): Instructions to set up an AWS Cloud CE in Seqera Platform
- [AWS Spot interruption management](https://docs.seqera.io//platform-enterprise_docs/compute-envs/aws-spot-interruptions.md): Managing AWS Spot Interruptions in Seqera Platform.
- [Azure Batch](https://docs.seqera.io//platform-enterprise_docs/compute-envs/azure-batch.md): Instructions to set up Azure Batch in Seqera Platform
- [Azure Cloud](https://docs.seqera.io//platform-enterprise_docs/compute-envs/azure-cloud.md): Instructions to set up an Azure Cloud compute environment in Seqera Platform
- [Amazon EKS](https://docs.seqera.io//platform-enterprise_docs/compute-envs/eks.md): Instructions to set up Amazon EKS in Seqera Platform
- [Google Kubernetes Engine](https://docs.seqera.io//platform-enterprise_docs/compute-envs/gke.md): Instructions to set up Google Kubernetes Engine in Seqera Platform
- [Google Cloud Batch](https://docs.seqera.io//platform-enterprise_docs/compute-envs/google-cloud-batch.md): Instructions to set up Google Cloud Batch in Seqera Platform
- [Google Cloud](https://docs.seqera.io//platform-enterprise_docs/compute-envs/google-cloud.md): Instructions to set up an Google Cloud CE in Seqera Platform
- [HPC compute environments](https://docs.seqera.io//platform-enterprise_docs/compute-envs/hpc.md): Instructions to set up HPC compute environments in Seqera Platform
- [Kubernetes](https://docs.seqera.io//platform-enterprise_docs/compute-envs/k8s.md): Instructions to set up Kubernetes in Seqera Platform
- [Compute environment overview](https://docs.seqera.io//platform-enterprise_docs/compute-envs/overview.md): Overview of compute environments in Seqera Platform
- [Tower Agent credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/agent_credentials.md): Instructions to create Tower Agent credentials in Seqera Platform.
- [AWS ECR credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/aws_registry_credentials.md): Instructions to create AWS ECR credentials in Seqera Platform.
- [Azure container registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/azure_registry_credentials.md): Instructions to create Azure container registry credentials in Seqera Platform.
- [Data repositories](https://docs.seqera.io//platform-enterprise_docs/credentials/data_repositories.md): Instructions for adding data repositories to Seqera Platform
- [Docker Hub credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/docker_hub_registry_credentials.md): Instructions to create Docker Hub credentials in Seqera Platform.
- [Gitea container registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/gitea_registry_credentials.md): Instructions to create GitHub container registry credentials in Seqera Platform.
- [GitHub container registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/github_registry_credentials.md): Instructions to create GitHub container registry credentials in Seqera Platform.
- [GitLab container registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/gitlab_registry_credentials.md): Instructions to create GitLab container registry credentials in Seqera Platform.
- [Google registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/google_registry_credentials.md): Instructions to create Google Cloud registry credentials in Seqera Platform.
- [Managed identities](https://docs.seqera.io//platform-enterprise_docs/credentials/managed_identities.md): Configure managed identities in Seqera Platform.
- [Credentials Overview](https://docs.seqera.io//platform-enterprise_docs/credentials/overview.md): Overview of credentials in Seqera Platform.
- [Quay container registry credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/quay_registry_credentials.md): Instructions to create Quay container registry credentials in Seqera Platform.
- [SSH credentials](https://docs.seqera.io//platform-enterprise_docs/credentials/ssh_credentials.md): Instructions to create SSH credentials in Seqera Platform.
- [Data Explorer](https://docs.seqera.io//platform-enterprise_docs/data/data-explorer.md): Using Seqera Data Explorer.
- [Data lineage](https://docs.seqera.io//platform-enterprise_docs/data/data-lineage.md): Using data lineage in Seqera Platform.
- [Datasets](https://docs.seqera.io//platform-enterprise_docs/data/datasets.md): Use datasets as pipeline inputs in Seqera Platform.
- [Data privacy](https://docs.seqera.io//platform-enterprise_docs/data-privacy/overview.md): The data Seqera Platform collects and stores
- [Source locations](https://docs.seqera.io//platform-enterprise_docs/enterprise/_images/README.md): The images under this folder are both generated from source files in the Seqera company Google Drive. If you're a Seqera employee, search for the f...
- [Cert_on_frontend](https://docs.seqera.io//platform-enterprise_docs/enterprise/_templates/nginx/cert_on_frontend.md): title: "cert_on_frontend"
- [Custom Content Security Policy headers](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/content-security-policy.md): Seqera Platform Content Security Policy headers
- [Custom AWS Batch launch container](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/custom-launch-container.md): Use a custom AWS Batch launch container
- [Firewall configuration](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/firewall-configuration.md): Configure your firewall to allow Seqera Cloud access
- [Manual AWS Batch configuration](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/manual-aws-batch-setup.md): Manual AWS Batch configuration
- [Azure Batch walkthrough](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/manual-azure-batch-setup.md): A tutorial for using advanced features of Azure Batch with Seqera Platform
- [Seqera Platform Monitoring](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/monitoring.md): A guide on relevant platform metrics
- [Legacy Seqera container image registries](https://docs.seqera.io//platform-enterprise_docs/enterprise/advanced-topics/seqera-container-images.md): Legacy Seqera container deployments
- [Email](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/email.md): Configure email-based authentication for Seqera Platform
- [Entra ID](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/entra.md): Configure Microsoft Entra ID as an identity provider for Seqera Platform
- [GitHub](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/github.md): Configure GitHub as an identity provider for Seqera Platform
- [Google](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/google.md): Configure Google as an identity provider for Seqera Platform
- [IdP claim mapping](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/claim-mapping.md): Configure your identity provider to include the groups claim in OIDC tokens issued to Seqera Platform Enterprise.
- [Manage your IdP group catalog](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/group-catalog/overview.md): Populate Seqera with your IdP's groups using SCIM push or manual entry.
- [SCIM provisioning with Entra ID](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/group-catalog/scim-entra-id.md): Configure Microsoft Entra ID to push group memberships to Seqera Platform Enterprise over SCIM 2.0.
- [SCIM provisioning with Okta](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/group-catalog/scim-okta.md): Configure Okta to push group memberships to Seqera Platform Enterprise over SCIM 2.0.
- [Multi-organization routing](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/multi-org-routing.md): How IdP delegation resolves users to organizations in single-organization and multi-organization Enterprise installations.
- [IdP delegation overview](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/idp-delegation/overview.md): Map Seqera teams to identity provider (IdP) groups so membership is controlled at the IdP and evaluated on every SSO login.
- [Keycloak](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/keycloak.md): Configure Keycloak as an identity provider for Seqera Platform
- [Okta](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/okta.md): Configure Okta as an identity provider for Seqera Platform
- [Authentication](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/authentication/overview.md): Configure authentication and identity providers for Seqera Platform
- [AWS Parameter Store](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/aws_parameter_store.md): Configure values for Seqera configuration with AWS Parameter Store
- [Mirroring container images](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/mirroring.md): Mirror Seqera container images to your own registry
- [Networking](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/networking.md): Seqera configuration options for networking
- [Configuration overview](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/overview.md): Overview of Seqera configuration options
- [Pipeline optimization](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/pipeline_optimization.md): Configure pipeline optimization in your Seqera Enterprise deployment.
- [Reverse proxy](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/reverse_proxy.md): Configuration options for reverse proxy connection
- [SSL/TLS](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/ssl_tls.md): Configure your Seqera instance to use SSL/TLS certificates for HTTPS
- [Wave containers](https://docs.seqera.io//platform-enterprise_docs/enterprise/configuration/wave.md): Configuring the Wave container service
- [Troubleshooting](https://docs.seqera.io//platform-enterprise_docs/enterprise/general_troubleshooting.md): Platform Enterprise troubleshooting guidance
- [Pipeline optimization: Docker Compose](https://docs.seqera.io//platform-enterprise_docs/enterprise/groundswell-docker-compose.md): Deploy pipeline optimization with Docker Compose
- [Pipeline Optimization: Helm](https://docs.seqera.io//platform-enterprise_docs/enterprise/groundswell-helm.md): Deploy Pipeline Optimization Enterprise on Kubernetes with Helm
- [Pipeline optimization: Kubernetes](https://docs.seqera.io//platform-enterprise_docs/enterprise/groundswell-kubernetes.md): Deploy pipeline optimization on Kubernetes
- [Pipeline optimization](https://docs.seqera.io//platform-enterprise_docs/enterprise/install-groundswell.md): Install pipeline optimization for Seqera Platform Enterprise
- [Platform](https://docs.seqera.io//platform-enterprise_docs/enterprise/install-platform.md): Install Seqera Platform Enterprise
- [Co-Scientist](https://docs.seqera.io//platform-enterprise_docs/enterprise/install-seqera-coscientist.md): Install and configure Co-Scientist for Seqera Platform Enterprise
- [Studios](https://docs.seqera.io//platform-enterprise_docs/enterprise/install-studios.md): Install Studios for Seqera Platform Enterprise
- [Enterprise installation](https://docs.seqera.io//platform-enterprise_docs/enterprise/overview.md): Platform Enterprise installation overview
- [Platform: Docker Compose](https://docs.seqera.io//platform-enterprise_docs/enterprise/platform-docker-compose.md): Deploy Seqera Platform Enterprise with Docker Compose
- [Platform: Helm](https://docs.seqera.io//platform-enterprise_docs/enterprise/platform-helm.md): Deploy Seqera Platform Enterprise on Kubernetes with Helm
- [Platform: Kubernetes](https://docs.seqera.io//platform-enterprise_docs/enterprise/platform-kubernetes.md): Deploy Seqera Platform Enterprise with Kubernetes
- [Studios: Docker Compose](https://docs.seqera.io//platform-enterprise_docs/enterprise/studios-docker-compose.md): Deploy Studios with Docker Compose
- [Studios: Helm](https://docs.seqera.io//platform-enterprise_docs/enterprise/studios-helm.md): Deploy Studios Enterprise on Kubernetes with Helm
- [Studios: Kubernetes](https://docs.seqera.io//platform-enterprise_docs/enterprise/studios-kubernetes.md): Deploy Studios on Kubernetes
- [Studios SSH configuration (public preview)](https://docs.seqera.io//platform-enterprise_docs/enterprise/studios-ssh.md): Configure SSH access for Studios (public preview)
- [Test deployment](https://docs.seqera.io//platform-enterprise_docs/enterprise/testing.md): Test your Seqera Platform Enterprise deployment after installation
- [Upgrade deployment](https://docs.seqera.io//platform-enterprise_docs/enterprise/upgrade.md): Guidance for upgrading to Platform Enterprise version 26.1
- [Default version compatibility](https://docs.seqera.io//platform-enterprise_docs/functionality_matrix/overview.md): Version compatibility for Seqera Platform, nf-launcher, Nextflow, Fusion, and the Connect client
- [Deploy Platform](https://docs.seqera.io//platform-enterprise_docs/getting-started/deployment-options.md): An overview of deployment versions and ways to run Seqera Platform.
- [Run a pipeline](https://docs.seqera.io//platform-enterprise_docs/getting-started/overview.md): An overview of Seqera Platform deployment versions and ways to run Seqera.
- [Production checklist](https://docs.seqera.io//platform-enterprise_docs/getting-started/production-checklist.md): A pre-production checklist for Seqera Platform.
- [Protein structure prediction](https://docs.seqera.io//platform-enterprise_docs/getting-started/proteinfold.md): An introduction to running nf-core/proteinfold in Seqera Platform
- [Add data](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/add-data.md): An introduction to adding pipeline input data in Seqera Platform
- [Add pipelines](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/add-pipelines.md): An introduction to adding pipelines to Seqera Platform workspaces
- [Automation](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/automation.md): An introduction to automation with APIs and CLI tools in Seqera Platform
- [Launch pipelines](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/launch-pipelines.md): An introduction to launching nf-core/rnaseq in the community/showcase workspace
- [Monitor runs](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/monitor-runs.md): Monitor pipeline runs from the Runs page, All runs page, and Dashboard in Seqera Platform
- [Pipeline optimization](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/pipeline-optimization.md): An introduction to pipeline optimization in Seqera Platform
- [Studios](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/studios.md): An introduction to Studios in Seqera Platform
- [View run information](https://docs.seqera.io//platform-enterprise_docs/getting-started/quickstart-demo/view-run-information.md): View pipeline run details in Seqera Platform
- [RNA-Seq](https://docs.seqera.io//platform-enterprise_docs/getting-started/rnaseq.md): An introduction to running nf-core/rnaseq in Seqera Platform
- [Studios for interactive analysis](https://docs.seqera.io//platform-enterprise_docs/getting-started/studios.md): Creating interactive analysis Studios for Jupyter, RStudio, VS Code, and more
- [Set up your workspace](https://docs.seqera.io//platform-enterprise_docs/getting-started/workspace-setup.md): Instructions to create an organization workspace and add participants in Seqera Platform.
- [Git integration](https://docs.seqera.io//platform-enterprise_docs/git/overview.md): Connecting to Git repositories in Seqera Platform.
- [Labels](https://docs.seqera.io//platform-enterprise_docs/labels/overview.md): Instructions for using labels in Seqera Platform.
- [Advanced options](https://docs.seqera.io//platform-enterprise_docs/launch/advanced.md): Advanced guide to launching Nextflow pipelines in Seqera Platform.
- [Nextflow cache and resume](https://docs.seqera.io//platform-enterprise_docs/launch/cache-resume.md): Guide to Nextflow cache and resume in Seqera Platform
- [Launch pipelines](https://docs.seqera.io//platform-enterprise_docs/launch/launchpad.md): Curate and launch workflows in Seqera Platform
- [Usage limits](https://docs.seqera.io//platform-enterprise_docs/limits/overview.md): Seqera Platform usage limits per organization and workspace
- [Audit logs](https://docs.seqera.io//platform-enterprise_docs/monitoring/audit-logs.md): An overview of application event audit logs in the Admin panel
- [Monitoring cloud costs](https://docs.seqera.io//platform-enterprise_docs/monitoring/cloud-costs.md): Guidelines for monitoring Seqera Platform cloud expenditure.
- [Dashboard](https://docs.seqera.io//platform-enterprise_docs/monitoring/dashboard.md): View pipeline run status overview in Seqera Platform.
- [Overview](https://docs.seqera.io//platform-enterprise_docs/monitoring/overview.md): Monitoring pipeline runs in Seqera Platform.
- [Run details](https://docs.seqera.io//platform-enterprise_docs/monitoring/run-details.md): Monitoring a Nextflow pipeline executed through Seqera Platform.
- [Custom roles](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/custom-roles.md): Introduction to custom roles in Seqera Platform.
- [Organizations](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/organizations.md): Manage organizations in Seqera Platform.
- [Personal profile and default settings](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/personal-profile.md): Manage your personal profile and default settings.
- [User roles](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/roles.md): Understand the various roles in Seqera Platform.
- [Teams](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/teams.md): Create and manage teams in a Seqera Platform Enterprise organization, including IdP-delegated teams.
- [Workspaces](https://docs.seqera.io//platform-enterprise_docs/orgs-and-teams/workspace-management.md): Manage users and teams for an organization in Seqera Platform.
- [Pipeline actions](https://docs.seqera.io//platform-enterprise_docs/pipeline-actions/overview.md): Automate executions with pipeline actions and webhooks in Seqera Platform.
- [Pipeline optimization](https://docs.seqera.io//platform-enterprise_docs/pipeline-optimization/overview.md): Optimize the resource usage of your pipelines to save time and money.
- [Pipeline schema](https://docs.seqera.io//platform-enterprise_docs/pipeline-schema/overview.md): Introduction to pipeline schema in Seqera Platform.
- [Overview](https://docs.seqera.io//platform-enterprise_docs/pipelines/overview.md): Introduction to pipelines in Seqera Platform.
- [Git revision management](https://docs.seqera.io//platform-enterprise_docs/pipelines/revision.md): Introduction to pipeline repository revision management in Seqera Platform.
- [Pipeline versioning](https://docs.seqera.io//platform-enterprise_docs/pipelines/versioning.md): Introduction to pipeline versioning in Seqera Platform.
- [Seqera Platform Enterprise](https://docs.seqera.io//platform-enterprise_docs/platform-enterprise.md): Introduction to Seqera Platform Enterprise.
- [Reports](https://docs.seqera.io//platform-enterprise_docs/reports/overview.md): Overview of pipeline reports in Seqera Platform.
- [Resource labels](https://docs.seqera.io//platform-enterprise_docs/resource-labels/overview.md): Instructions to use resource labels in Seqera Platform.
- [Secrets](https://docs.seqera.io//platform-enterprise_docs/secrets/overview.md): Instructions to use secrets in Seqera Platform.
- [Commands](https://docs.seqera.io//platform-enterprise_docs/seqerakit/commands.md): Seqerakit command options
- [Installation](https://docs.seqera.io//platform-enterprise_docs/seqerakit/installation.md): Seqerakit installation options
- [Templates](https://docs.seqera.io//platform-enterprise_docs/seqerakit/templates.md): Seqerakit YAML configuration file templates and instructions
- [YAML configuration](https://docs.seqera.io//platform-enterprise_docs/seqerakit/yaml-configuration.md): seqerakit YAML configuration file options
- [Custom container template](https://docs.seqera.io//platform-enterprise_docs/studios/add-studio-custom-container.md): Add a Studio in Platform.
- [Import from Git repository](https://docs.seqera.io//platform-enterprise_docs/studios/add-studio-git-repo.md): Add a Studio in Platform.
- [Seqera-provided container template](https://docs.seqera.io//platform-enterprise_docs/studios/add-studio-provided-template.md): Add a Studio in Platform.
- [Add a Studio](https://docs.seqera.io//platform-enterprise_docs/studios/add-studio.md): Add a Studio in Platform.
- [Connect changelog](https://docs.seqera.io//platform-enterprise_docs/studios/connect.md): :::note
- [Container image templates](https://docs.seqera.io//platform-enterprise_docs/studios/container-images.md): Use container images with Studios.
- [Custom environments](https://docs.seqera.io//platform-enterprise_docs/studios/custom-envs.md): Custom environments for Studios
- [Example custom Studios](https://docs.seqera.io//platform-enterprise_docs/studios/example-studios.md): Example Dockerfiles and pre-built container images for running custom applications in Studios.
- [Manage Studios](https://docs.seqera.io//platform-enterprise_docs/studios/managing.md): Manage Studio sessions.
- [Overview](https://docs.seqera.io//platform-enterprise_docs/studios/overview.md): Interactive analysis environments in Seqera Platform
- [Tower Agent](https://docs.seqera.io//platform-enterprise_docs/supported_software/agent/overview.md): Use Tower Agent to connect Seqera Platform to HPC clusters that do not allow inbound SSH connections.
- [Illumina DRAGEN](https://docs.seqera.io//platform-enterprise_docs/supported_software/dragen/overview.md): Instructions to integrate Illumina DRAGEN with Seqera Platform.
- [Fusion v2 file system](https://docs.seqera.io//platform-enterprise_docs/supported_software/fusion/overview.md): Fusion file system
- [Developer tools](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/api_and_cli.md): API and CLI troubleshooting with Seqera Platform.
- [AWS](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/aws_troubleshooting.md): AWS troubleshooting with Seqera Platform.
- [Azure](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/azure_troubleshooting.md): Azure troubleshooting with Seqera Platform.
- [Datasets](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/datasets_troubleshooting.md): Dataset troubleshooting with Seqera Platform.
- [Nextflow](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/nextflow.md): Nextflow troubleshooting with Seqera Platform.
- [Resource labels](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/resource-labels.md): Troubleshooting resource labels in Seqera Platform
- [Studios](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/studios_troubleshooting.md): Studios troubleshooting with Seqera Platform.
- [General troubleshooting](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md): Troubleshooting Seqera Platform
- [Workspaces](https://docs.seqera.io//platform-enterprise_docs/troubleshooting_and_faqs/workspaces_troubleshooting.md): Workspaces troubleshooting with Seqera Platform.

# Seqera Platform Cloud

> Documentation for Seqera Platform Cloud.

This file contains links to Seqera Platform Cloud documentation following the llmstxt.org standard.

## Table of Contents

- [Billing and credit management](https://docs.seqera.io//platform-cloud/docs/administration/credit-management.md): Manage Seqera credits across Seqera Compute and Co-Scientist.
- [Cloud changelog](https://docs.seqera.io//platform-cloud/docs/cloud/changelog.md): Seqera Platform Cloud changelog
- [Release notes for Seqera Cloud version 24.1.x](https://docs.seqera.io//platform-cloud/docs/cloud/cloud_latest.md): Data Studios is now publicly available for Seqera Cloud.
- [Authentication](https://docs.seqera.io//platform-cloud/docs/co-scientist/authentication.md): Log in, log out, and manage organizations and tokens in the Seqera CLI
- [Coding agents](https://docs.seqera.io//platform-cloud/docs/co-scientist/coding-agents.md): Install Co-Scientist as a skill so your coding agent can drive Seqera Platform
- [Command approval](https://docs.seqera.io//platform-cloud/docs/co-scientist/command-approval.md): Control which local commands require user approval in Co-Scientist
- [Using Co-Scientist](https://docs.seqera.io//platform-cloud/docs/co-scientist/configuration.md): Use Co-Scientist day to day in the Seqera CLI
- [Credits](https://docs.seqera.io//platform-cloud/docs/co-scientist/credits.md): Co-Scientist credits and how to request more
- [Co-Scientist in Seqera CLI](https://docs.seqera.io//platform-cloud/docs/co-scientist/index.md): AI-powered assistant for bioinformatics workflows and Seqera Platform
- [Installation](https://docs.seqera.io//platform-cloud/docs/co-scientist/installation.md): Install and configure the Seqera CLI
- [Modes](https://docs.seqera.io//platform-cloud/docs/co-scientist/modes.md): Work in Co-Scientist's build, plan, and goal modes
- [Code intelligence](https://docs.seqera.io//platform-cloud/docs/co-scientist/nextflow-lsp.md): Use language-server code intelligence in Co-Scientist
- [Projects](https://docs.seqera.io//platform-cloud/docs/co-scientist/projects.md): Organize workspace resources into projects using Seqera Platform labels
- [Quickstart](https://docs.seqera.io//platform-cloud/docs/co-scientist/quickstart.md): Run your first Co-Scientist session in the Seqera CLI
- [CLI](https://docs.seqera.io//platform-cloud/docs/co-scientist/reference/cli.md): Seqera CLI commands and options for Co-Scientist
- [Environment variables](https://docs.seqera.io//platform-cloud/docs/co-scientist/reference/environment-variables.md): Environment variables for authenticating and configuring the Seqera CLI
- [Reference](https://docs.seqera.io//platform-cloud/docs/co-scientist/reference/index.md): Reference material for the Seqera CLI and Co-Scientist
- [Skills](https://docs.seqera.io//platform-cloud/docs/co-scientist/reference/skills-reference.md): Built-in skills, slash commands, and session limits for the Seqera CLI
- [Sessions](https://docs.seqera.io//platform-cloud/docs/co-scientist/sessions.md): Start, continue, resume, and exit Co-Scientist sessions, and run non-interactively
- [Antigravity/Gemini](https://docs.seqera.io//platform-cloud/docs/co-scientist/skill-antigravity.md): Install and maintain the Co-Scientist skill for Google's Antigravity/Gemini IDE
- [Claude Code](https://docs.seqera.io//platform-cloud/docs/co-scientist/skill-claude-code.md): Install and maintain the Co-Scientist skill for Claude Code
- [Codex](https://docs.seqera.io//platform-cloud/docs/co-scientist/skill-codex.md): Install and maintain the Co-Scientist skill for Codex
- [GitHub Copilot](https://docs.seqera.io//platform-cloud/docs/co-scientist/skill-github-copilot.md): Install and maintain the Co-Scientist skill for GitHub Copilot
- [Other coding agents](https://docs.seqera.io//platform-cloud/docs/co-scientist/skill-other-agents.md): Install and maintain the Co-Scientist skill for other coding agents
- [Skills configuration](https://docs.seqera.io//platform-cloud/docs/co-scientist/skills.md): Discover, create, and install skills in the Seqera CLI
- [Use cases](https://docs.seqera.io//platform-cloud/docs/co-scientist/use-cases.md): Common tasks you can do with Co-Scientist, with example prompts
- [AWS Batch](https://docs.seqera.io//platform-cloud/docs/compute-envs/aws-batch.md): Instructions to set up AWS Batch in Seqera Platform
- [AWS Cloud](https://docs.seqera.io//platform-cloud/docs/compute-envs/aws-cloud.md): Instructions to set up an AWS Cloud CE in Seqera Platform
- [AWS Spot interruption management](https://docs.seqera.io//platform-cloud/docs/compute-envs/aws-spot-interruptions.md): Managing AWS Spot Interruptions in Seqera Platform.
- [Azure Batch](https://docs.seqera.io//platform-cloud/docs/compute-envs/azure-batch.md): Instructions to set up Azure Batch in Seqera Platform
- [Azure Cloud](https://docs.seqera.io//platform-cloud/docs/compute-envs/azure-cloud.md): Instructions to set up an Azure Cloud compute environment in Seqera Platform
- [Amazon EKS](https://docs.seqera.io//platform-cloud/docs/compute-envs/eks.md): Instructions to set up Amazon EKS in Seqera Platform
- [Google Kubernetes Engine](https://docs.seqera.io//platform-cloud/docs/compute-envs/gke.md): Instructions to set up Google Kubernetes Engine in Seqera Platform
- [Google Cloud Batch](https://docs.seqera.io//platform-cloud/docs/compute-envs/google-cloud-batch.md): Instructions to set up Google Cloud Batch in Seqera Platform
- [Google Cloud](https://docs.seqera.io//platform-cloud/docs/compute-envs/google-cloud.md): Instructions to set up an Google Cloud CE in Seqera Platform
- [HPC compute environments](https://docs.seqera.io//platform-cloud/docs/compute-envs/hpc.md): Instructions to set up HPC compute environments in Seqera Platform
- [Intelligent Compute](https://docs.seqera.io//platform-cloud/docs/compute-envs/intelligent-compute.md): Set up Seqera Intelligent Compute on an AWS Cloud compute environment
- [Kubernetes](https://docs.seqera.io//platform-cloud/docs/compute-envs/k8s.md): Instructions to set up Kubernetes in Seqera Platform
- [Compute environment overview](https://docs.seqera.io//platform-cloud/docs/compute-envs/overview.md): Overview of compute environments in Seqera Platform
- [Compute environment pre-flight checks](https://docs.seqera.io//platform-cloud/docs/compute-envs/preflight-checks.md): How Seqera Platform continuously validates compute environments and what to do when a check fails
- [Seqera Compute](https://docs.seqera.io//platform-cloud/docs/compute-envs/seqera-compute.md): Instructions to set up Seqera Compute in Seqera Platform
- [Tower Agent credentials](https://docs.seqera.io//platform-cloud/docs/credentials/agent_credentials.md): Create Tower Agent credentials in Seqera Platform.
- [AWS ECR credentials](https://docs.seqera.io//platform-cloud/docs/credentials/aws_registry_credentials.md): Create AWS ECR credentials in Seqera Platform.
- [Azure container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/azure_registry_credentials.md): Create Azure container registry credentials in Seqera Platform.
- [Container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/container_registry_credentials.md): Configure container registry credentials for the Wave container service in Seqera Platform.
- [Data repositories](https://docs.seqera.io//platform-cloud/docs/credentials/data_repositories.md): Add data repositories to Seqera Platform
- [Docker Hub credentials](https://docs.seqera.io//platform-cloud/docs/credentials/docker_hub_registry_credentials.md): Create Docker Hub credentials in Seqera Platform.
- [Gitea container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/gitea_registry_credentials.md): Create GitHub container registry credentials in Seqera Platform.
- [GitHub container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/github_registry_credentials.md): Create GitHub container registry credentials in Seqera Platform.
- [GitLab container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/gitlab_registry_credentials.md): Create GitLab container registry credentials in Seqera Platform.
- [Google registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/google_registry_credentials.md): Create Google Cloud registry credentials in Seqera Platform.
- [Managed identities](https://docs.seqera.io//platform-cloud/docs/credentials/managed_identities.md): Configure managed identities in Seqera Platform.
- [Credentials overview](https://docs.seqera.io//platform-cloud/docs/credentials/overview.md): Learn about credentials in Seqera Platform.
- [Quay container registry credentials](https://docs.seqera.io//platform-cloud/docs/credentials/quay_registry_credentials.md): Create Quay container registry credentials in Seqera Platform.
- [SSH credentials](https://docs.seqera.io//platform-cloud/docs/credentials/ssh_credentials.md): Create SSH credentials in Seqera Platform.
- [Data Explorer](https://docs.seqera.io//platform-cloud/docs/data/data-explorer.md): Using Seqera Data Explorer.
- [Data lineage](https://docs.seqera.io//platform-cloud/docs/data/data-lineage.md): Using data lineage in Seqera Platform.
- [Datasets](https://docs.seqera.io//platform-cloud/docs/data/datasets.md): Use datasets as pipeline inputs in Seqera Platform.
- [Data privacy](https://docs.seqera.io//platform-cloud/docs/data-privacy/overview.md): The data Seqera Platform collects and stores
- [Manual AWS Batch configuration](https://docs.seqera.io//platform-cloud/docs/enterprise/advanced-topics/manual-aws-batch-setup.md): Manual AWS Batch configuration
- [Azure Batch compute environment setup](https://docs.seqera.io//platform-cloud/docs/enterprise/advanced-topics/manual-azure-batch-setup.md): A tutorial for using Azure Batch with Seqera Platform
- [Default version compatibility](https://docs.seqera.io//platform-cloud/docs/functionality_matrix/overview.md): Version compatibility for Seqera Platform, nf-launcher, Nextflow, Fusion, and the Connect client
- [Deployment options](https://docs.seqera.io//platform-cloud/docs/getting-started/deployment-options.md): Seqera Platform deployment options and ways to access your Seqera instance.
- [Run a pipeline](https://docs.seqera.io//platform-cloud/docs/getting-started/overview.md): An overview of Seqera Platform deployment versions and ways to run Seqera.
- [Protein structure prediction](https://docs.seqera.io//platform-cloud/docs/getting-started/proteinfold.md): An introduction to running nf-core/proteinfold in Seqera Platform
- [Add data](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/add-data.md): An introduction to adding pipeline input data in Seqera Platform
- [Add pipelines](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/add-pipelines.md): An introduction to adding pipelines to Seqera Platform workspaces
- [Automation](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/automation.md): An introduction to automation with APIs and CLI tools in Seqera Platform
- [Community Showcase](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/comm-showcase.md): Seqera Cloud Community showcase workspace walkthrough
- [Launch pipelines](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/launch-pipelines.md): An introduction to launching nf-core/rnaseq in the community/showcase workspace
- [Monitor runs](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/monitor-runs.md): Monitor pipeline runs from the Runs page, All runs page, and Dashboard in Seqera Platform
- [Pipeline optimization](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/pipeline-optimization.md): An introduction to pipeline optimization in Seqera Platform
- [Studios](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/studios.md): An introduction to Studios in Seqera Platform
- [View run information](https://docs.seqera.io//platform-cloud/docs/getting-started/quickstart-demo/view-run-information.md): View pipeline run details in Seqera Platform
- [RNA-Seq](https://docs.seqera.io//platform-cloud/docs/getting-started/rnaseq.md): An introduction to running nf-core/rnaseq in Seqera Platform
- [Single sign-on (SSO)](https://docs.seqera.io//platform-cloud/docs/getting-started/single-sign-on.md): Configure single sign-on for a Seqera Platform Cloud organization.
- [Studios for interactive analysis](https://docs.seqera.io//platform-cloud/docs/getting-started/studios.md): Creating interactive analysis Studios for Jupyter, R-IDE, VS Code, and more
- [Set up your workspace](https://docs.seqera.io//platform-cloud/docs/getting-started/workspace-setup.md): Create an organization workspace and add participants in Seqera Platform.
- [Git integration](https://docs.seqera.io//platform-cloud/docs/git/overview.md): Connecting to Git repositories in Seqera Platform and Co-Scientist.
- [Labels](https://docs.seqera.io//platform-cloud/docs/labels/overview.md): Instructions for using labels in Nextflow Tower.
- [Advanced options](https://docs.seqera.io//platform-cloud/docs/launch/advanced.md): Advanced guide to launching Nextflow pipelines in Seqera Platform.
- [Nextflow cache and resume](https://docs.seqera.io//platform-cloud/docs/launch/cache-resume.md): Guide to Nextflow cache and resume in Seqera Platform
- [Launch pipelines](https://docs.seqera.io//platform-cloud/docs/launch/launchpad.md): Curate and launch pipelines in Seqera Platform
- [Usage limits](https://docs.seqera.io//platform-cloud/docs/limits/overview.md): Seqera Platform usage limits per organization and workspace
- [Monitoring cloud costs](https://docs.seqera.io//platform-cloud/docs/monitoring/cloud-costs.md): Guidelines for monitoring Seqera Platform cloud expenditure
- [Dashboard](https://docs.seqera.io//platform-cloud/docs/monitoring/dashboard.md): View pipeline run status overview in Seqera Platform.
- [Overview](https://docs.seqera.io//platform-cloud/docs/monitoring/overview.md): Monitoring pipeline runs in Seqera Platform.
- [Run details](https://docs.seqera.io//platform-cloud/docs/monitoring/run-details.md): Monitoring a Nextflow pipeline executed through Seqera Platform.
- [Custom roles](https://docs.seqera.io//platform-cloud/docs/orgs-and-teams/custom-roles.md): Introduction to custom roles in Seqera Platform.
- [Organizations](https://docs.seqera.io//platform-cloud/docs/orgs-and-teams/organizations.md): Manage organizations in Seqera Platform.
- [Personal profile and default settings](https://docs.seqera.io//platform-cloud/docs/orgs-and-teams/personal-profile.md): Manage your personal profile and default settings.
- [User roles](https://docs.seqera.io//platform-cloud/docs/orgs-and-teams/roles.md): Understand the various roles in Seqera Platform.
- [Workspaces](https://docs.seqera.io//platform-cloud/docs/orgs-and-teams/workspace-management.md): Manage users and teams for an organization in Seqera Platform.
- [Pipeline actions](https://docs.seqera.io//platform-cloud/docs/pipeline-actions/overview.md): Automate executions with pipeline actions and webhooks in Seqera Platform.
- [Pipeline optimization](https://docs.seqera.io//platform-cloud/docs/pipeline-optimization/overview.md): Optimize the resource usage of your pipelines to save time and money.
- [Pipeline schema](https://docs.seqera.io//platform-cloud/docs/pipeline-schema/overview.md): Introduction to pipeline schema in Seqera Platform.
- [Overview](https://docs.seqera.io//platform-cloud/docs/pipelines/overview.md): Introduction to pipelines in Seqera Platform.
- [Git revision management](https://docs.seqera.io//platform-cloud/docs/pipelines/revision.md): Introduction to pipeline repository revision management in Seqera Platform.
- [Pipeline versioning](https://docs.seqera.io//platform-cloud/docs/pipelines/versioning.md): Introduction to pipeline versioning in Seqera Platform.
- [Seqera Platform Cloud](https://docs.seqera.io//platform-cloud/docs/platform-cloud.md): Introduction to Seqera Platform Cloud.
- [Explore Seqera Cloud](https://docs.seqera.io//platform-cloud/docs/quickstart.md): Explore your free workspace resources and launch your first pipelines with Seqera Compute.
- [Reports](https://docs.seqera.io//platform-cloud/docs/reports/overview.md): Overview of pipeline reports in Seqera Platform.
- [Resource labels](https://docs.seqera.io//platform-cloud/docs/resource-labels/overview.md): Instructions to use resource labels in Seqera Platform.
- [Secrets](https://docs.seqera.io//platform-cloud/docs/secrets/overview.md): Instructions to use secrets in Seqera Platform.
- [nf-core Tools](https://docs.seqera.io//platform-cloud/docs/seqera-mcp/nfcore-tools.md): Search and explore nf-core bioinformatics modules and get analysis recommendations
- [Seqera MCP](https://docs.seqera.io//platform-cloud/docs/seqera-mcp/overview.md): Connect AI assistants to Seqera Platform using the Model Context Protocol
- [Seqera Platform Tools](https://docs.seqera.io//platform-cloud/docs/seqera-mcp/seqera-tools.md): Manage workflows, compute environments, and containers through Seqera Platform
- [SRA Tools](https://docs.seqera.io//platform-cloud/docs/seqera-mcp/sra-tools.md): Search and retrieve sequencing data from NCBI SRA, EBI ENA, and GEO databases
- [Commands](https://docs.seqera.io//platform-cloud/docs/seqerakit/commands.md): Seqerakit command options
- [Installation](https://docs.seqera.io//platform-cloud/docs/seqerakit/installation.md): Seqerakit installation options
- [Templates](https://docs.seqera.io//platform-cloud/docs/seqerakit/templates.md): Seqerakit YAML configuration file templates and instructions
- [YAML configuration](https://docs.seqera.io//platform-cloud/docs/seqerakit/yaml-configuration.md): seqerakit YAML configuration file options
- [Custom container template](https://docs.seqera.io//platform-cloud/docs/studios/add-studio-custom-container.md): Add a Studio with a custom container template in Seqera Platform.
- [Import from a Git repository](https://docs.seqera.io//platform-cloud/docs/studios/add-studio-git-repo.md): Add a Studio from a Git repository in Seqera Platform.
- [Seqera-provided container template](https://docs.seqera.io//platform-cloud/docs/studios/add-studio-provided-template.md): Add a Studio with a Seqera-provided container template in Seqera Platform.
- [Add a Studio](https://docs.seqera.io//platform-cloud/docs/studios/add-studio.md): Add a Studio in Platform.
- [Connect changelog](https://docs.seqera.io//platform-cloud/docs/studios/connect.md): :::note
- [Container image templates](https://docs.seqera.io//platform-cloud/docs/studios/container-images.md): Use container images with Studios.
- [Custom environments](https://docs.seqera.io//platform-cloud/docs/studios/custom-envs.md): Custom environments for Studios
- [Example custom Studios](https://docs.seqera.io//platform-cloud/docs/studios/example-studios.md): Example Dockerfiles and pre-built container images for running custom applications in Studios.
- [Manage Studios](https://docs.seqera.io//platform-cloud/docs/studios/managing.md): Manage Studio sessions.
- [Overview](https://docs.seqera.io//platform-cloud/docs/studios/overview.md): Interactive analysis environments in Seqera Platform
- [Tower Agent](https://docs.seqera.io//platform-cloud/docs/supported_software/agent/overview.md): Use Tower Agent to connect Seqera Platform to HPC clusters that do not allow inbound SSH connections.
- [Illumina DRAGEN](https://docs.seqera.io//platform-cloud/docs/supported_software/dragen/overview.md): Instructions to integrate Illumina DRAGEN with Seqera Platform.
- [Fusion v2 file system](https://docs.seqera.io//platform-cloud/docs/supported_software/fusion/overview.md): Fusion file system
- [Developer tools](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/api_and_cli.md): API and CLI troubleshooting with Seqera Platform.
- [AWS](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/aws_troubleshooting.md): AWS troubleshooting with Seqera Platform.
- [Azure](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/azure_troubleshooting.md): Azure troubleshooting with Seqera Platform.
- [Datasets](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/datasets_troubleshooting.md): Dataset troubleshooting with Seqera Platform.
- [Nextflow](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/nextflow.md): Nextflow troubleshooting with Seqera Platform.
- [Resource labels](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/resource-labels.md): Troubleshooting resource labels in Seqera Platform
- [Co-Scientist](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/seqera-ai.md): Co-Scientist troubleshooting.
- [Single sign-on](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/sso_troubleshooting.md): Single sign-on (SSO) troubleshooting with Seqera Platform.
- [Studios](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/studios_troubleshooting.md): Studios troubleshooting with Seqera Platform.
- [General](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md): Troubleshooting Seqera Platform
- [Workspaces](https://docs.seqera.io//platform-cloud/docs/troubleshooting_and_faqs/workspaces_troubleshooting.md): Workspaces troubleshooting with Seqera Platform.

# Seqera Platform CLI

> Documentation for the Seqera Platform command-line interface.

This file contains links to Seqera Platform CLI documentation following the llmstxt.org standard.

## Table of Contents

- [Command Reference](https://docs.seqera.io//platform-cli-docs/docs/commands-reference.md): Complete reference for Seqera Platform CLI commands
- [Installation](https://docs.seqera.io//platform-cli-docs/docs/installation.md): Seqera Platform CLI installation and configuration instructions.
- [Overview](https://docs.seqera.io//platform-cli-docs/docs/overview.md): Seqera Platform CLI overview.
- [tw actions](https://docs.seqera.io//platform-cli-docs/docs/reference/actions.md): Manage pipeline actions
- [tw collaborators](https://docs.seqera.io//platform-cli-docs/docs/reference/collaborators.md): Manage organization collaborators
- [tw compute-envs](https://docs.seqera.io//platform-cli-docs/docs/reference/compute-envs.md): Manage compute environments.
- [tw credentials](https://docs.seqera.io//platform-cli-docs/docs/reference/credentials.md): Manage workspace credentials
- [tw data-links](https://docs.seqera.io//platform-cli-docs/docs/reference/data-links.md): Manage data links
- [tw datasets](https://docs.seqera.io//platform-cli-docs/docs/reference/datasets.md): Manage datasets
- [tw info](https://docs.seqera.io//platform-cli-docs/docs/reference/info.md): Show system info and health status
- [tw labels](https://docs.seqera.io//platform-cli-docs/docs/reference/labels.md): Manage workspace labels
- [tw launch](https://docs.seqera.io//platform-cli-docs/docs/reference/launch.md): Launch a pipeline
- [tw members](https://docs.seqera.io//platform-cli-docs/docs/reference/members.md): Manage organization members
- [tw organizations](https://docs.seqera.io//platform-cli-docs/docs/reference/organizations.md): Manage organizations
- [tw participants](https://docs.seqera.io//platform-cli-docs/docs/reference/participants.md): Manage workspace participants
- [tw pipeline-schemas](https://docs.seqera.io//platform-cli-docs/docs/reference/pipeline-schemas.md): Manage pipeline schemas
- [tw pipelines](https://docs.seqera.io//platform-cli-docs/docs/reference/pipelines.md): Manage pipelines
- [tw runs](https://docs.seqera.io//platform-cli-docs/docs/reference/runs.md): Manage pipeline runs
- [tw secrets](https://docs.seqera.io//platform-cli-docs/docs/reference/secrets.md): Manage secrets
- [tw studios](https://docs.seqera.io//platform-cli-docs/docs/reference/studios.md): Manage studios
- [tw teams](https://docs.seqera.io//platform-cli-docs/docs/reference/teams.md): Manage teams
- [tw workspaces](https://docs.seqera.io//platform-cli-docs/docs/reference/workspaces.md): Manage workspaces

# MultiQC

> Documentation for MultiQC

This file contains links to MultiQC documentation following the llmstxt.org standard.

## Table of Contents

- [AI summaries](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/ai/index.md): Using AI to summarise MultiQC reports
- [MultiQC Configuration Reference](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/config_schema.md): This document describes all configuration options available in MultiQC.
- [Custom content](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/custom_content/index.md): Report on your data, even without a MultiQC module
- [Breaking changes](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/compatibility.md): Notes about major MultiQC updates
- [Contributing](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/contributing.md): Guides for how to contribute to the MultiQC code base
- [Development](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/index.md): Building MultiQC modules and templates
- [Writing new modules](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/modules.md): Adding support for a new tool
- [Plotting functions](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/plots.md): Visualising your data
- [MultiQC Plugins](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/plugins.md): Extending core functionality with plugins
- [Writing new templates](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/development/templates.md): Making MultiQC reports your own
- [Configuration](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/getting_started/config.md): Settings to tweak how MultiQC works
- [Config Wizard](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/getting_started/config_wizard.md): Build a multiqc_config.yaml in your browser, with live schema validation and a YAML editor.
- [Installation](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/getting_started/installation.md): How to install MultiQC on your system
- [Quick start](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/getting_started/quick_start.md): A tutorial with a typical setup for people in a rush.
- [Running MultiQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/getting_started/running_multiqc.md): Generating MultiQC reports from your data
- [MultiQC overview](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/index.md): How to install MultiQC on your system
- [Adapter Removal](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/adapterremoval.md): Removes adapter sequences, trims low quality bases from 3' ends, or merges overlapping pairs into consensus.
- [AfterQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/afterqc.md): Automatic filtering, trimming, error removing, and quality control for FastQ data.
- [Anglerfish](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/anglerfish.md): Quality controls Illumina libraries sequenced on Oxford Nanopore flowcells.
- [ATAQV](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ataqv.md): Toolkit for quality control and visualization of ATAC-seq data.
- [Bakta](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bakta.md): Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
- [Bamdst](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bamdst.md): Lightweight tool to stat the depth coverage of target regions of BAM file(s).
- [Bamtools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bamtools.md): Provides both a programmer's API and an end-user's toolkit for handling BAM files.
- [Bases2Fastq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bases2fastq.md): Demultiplexes and converts Element AVITI base calls into FASTQ files.
- [BBDuk](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bbduk.md): Common data-quality-related trimming, filtering, and masking operations with a kmer based approach.
- [BBTools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bbmap.md): Pre-processing, assembly, alignment, and statistics tools for DNA/RNA sequencing reads.
- [Bcftools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bcftools.md): Utilities for variant calling and manipulating VCFs and BCFs.
- [bcl2fastq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bcl2fastq.md): Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.
- [BCL Convert](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bclconvert.md): Demultiplexes data and converts BCL files to FASTQ file formats for downstream analysis.
- [biobambam2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/biobambam2.md): Tools for early stage alignment file processing.
- [BioBloom Tools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/biobloomtools.md): Assigns reads to different references using bloom filters. This is faster than alignment and can be used for contamination detection.
- [BISCUIT](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/biscuit.md): Maps bisulfite converted DNA sequence reads and determines cytosine methylation states.
- [Bismark](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bismark.md): Maps bisulfite converted sequence reads and determine cytosine methylation states.
- [Bowtie 1](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bowtie1.md): Ultrafast, memory-efficient short read aligner.
- [Bowtie 2 / HiSAT2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bowtie2.md): Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.
- [BUSCO](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/busco.md): Assesses genome assembly and annotation completeness.
- [Bustools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/bustools.md): Tools for BUS files - a file format for single-cell RNA-seq data designed to facilitate the development of modular workflows for data processing.
- [CCS](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ccs.md): PacBio tool that generates highly accurate single-molecule consensus reads (HiFi Reads).
- [Cell Ranger](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/cellranger.md): Analyzes single cell expression or VDJ data produced by 10X Genomics.
- [Cell Ranger ARC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/cellranger_arc.md): Analyzes single-cell multiome ATAC and gene expression data produced by 10X Genomics.
- [cells2stats](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/cells2stats.md): Generate output files and statistics from Element Biosciences Teton cytoprofiling assays.
- [CheckAtlas](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/checkatlas.md): A one-liner tool for quality control of your single-cell atlases.
- [CheckM](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/checkm.md): Estimates genome completeness and contamination based on the presence or absence of marker genes.
- [CheckM2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/checkm2.md): Assesses microbial genome quality using machine learning.
- [CheckQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/checkqc.md): Checks a set of quality criteria against an Illumina runfolder.
- [ClipAndMerge](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/clipandmerge.md): Adapter clipping and read merging for ancient DNA data.
- [Cluster Flow](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/clusterflow.md): Simple and flexible bioinformatics pipeline tool.
- [Conpair](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/conpair.md): Estimates concordance and contamination for tumor–normal pairs.
- [Cutadapt](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/cutadapt.md): Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.
- [DamageProfiler](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/damageprofiler.md): DNA damage pattern retrieval for ancient DNA analysis.
- [Deacon](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/deacon.md): Search and depletion of FASTA/FASTQ files and streams using accelerated minimizer matching.
- [DeDup](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/dedup.md): Improved Duplicate Removal for merged/collapsed reads in ancient DNA analysis.
- [deepTools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/deeptools.md): Tools to process and analyze deep sequencing data.
- [DIAMOND](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/diamond.md): Sequence aligner for protein and translated DNA searches, a drop-in replacement for the NCBI BLAST.
- [Disambiguate](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/disambiguate.md): Disambiguate reads aligned to two different species (e.g. human and mouse).
- [DRAGEN](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/dragen.md): Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.
- [DRAGEN-FastQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/dragen_fastqc.md): Illumina Bio-IT Platform that uses FPGA for secondary analysis of sequencing data.
- [eigenstratdatabasetools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/eigenstratdatabasetools.md): Tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.
- [fastp](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/fastp.md): All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).
- [FastQ Screen](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/fastq_screen.md): Screens a library of sequences in FastQ format against a set of sequence databases to see if the composition of the library matches with what you e...
- [FastQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/fastqc.md): Quality control tool for high throughput sequencing data.
- [FastQE](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/fastqe.md): Uses emoji to represent FASTQ sequence quality scores.
- [featureCounts](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/featurecounts.md): Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
- [fgbio](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/fgbio.md): Processing and evaluating data containing UMIs.
- [Filtlong](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/filtlong.md): Filters long reads by quality.
- [FLASh](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/flash.md): Merges paired-end reads from next-generation sequencing experiments.
- [Flexbar](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/flexbar.md): Barcode and adapter removal tool.
- [Freyja](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/freyja.md): Recovers relative lineage abundances from mixed SARS-CoV-2 samples.
- [Ganon](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ganon.md): Metagenomics classification: quickly assigns sequence fragments to their closest reference among thousands of references via Interleaved Bloom Filt...
- [GATK](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/gatk.md): Wide variety of tools with a primary focus on variant discovery and genotyping.
- [GffCompare](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/gffcompare.md): Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.
- [GLIMPSE](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/glimpse.md): Low-coverage whole genome sequencing imputation.
- [goleft indexcov](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/goleft_indexcov.md): Quickly estimate coverage from a whole-genome bam index, providing 16KB resolution.
- [GoPeaks](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/gopeaks.md): Calls peaks in CUT&TAG/CUT&RUN datasets.
- [GTDB-Tk](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/gtdbtk.md): Assigns objective taxonomic classifications to bacterial and archaeal genomes.
- [Haplocheck](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/haplocheck.md): Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.
- [hap.py](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/happy.md): Benchmarks variant calls against gold standard truth datasets.
- [HiCExplorer](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hicexplorer.md): Hi-C analysis from processing to visualization.
- [HiC-Pro](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hicpro.md): Pipeline for Hi-C data processing.
- [hicstuff](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hicstuff.md): Hi-C pipeline that generates contact maps from sequencing reads.
- [HiCUP](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hicup.md): Mapping and quality control on Hi-C data.
- [HiFi-Trimmer](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hifi_trimmer.md): Filters and trims adapter sequences from HiFi reads using BLAST.
- [HiFiasm](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hifiasm.md): Haplotype-resolved assembler for accurate Hifi reads.
- [HISAT2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hisat2.md): Maps DNA or RNA reads against a genome or a population of genomes.
- [HOMER](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/homer.md): Motif discovery and next-gen sequencing analysis.
- [HOPS](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hops.md): Ancient DNA characteristics screening tool of output from the metagenomic aligner MALT.
- [Hostile](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/hostile.md): Removes host sequences from short and long read (meta)genomes, from paired or unpaired fastq[.gz].
- [HTSeq Count](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/htseq.md): Part of the HTSeq package: counts reads covering specified genomic features.
- [HUMID](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/humid.md): Reference-free tool to quickly remove duplicates from FastQ files, with or without UMIs.
- [Illumina InterOp Statistics](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/interop.md): Reading and writing InterOp metric files.
- [Iso-Seq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/isoseq.md): Identifies transcripts in PacBio single-molecule sequencing data (HiFi reads).
- [iVar](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ivar.md): Functions for viral amplicon-based sequencing.
- [JCVI Genome Annotation](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/jcvi.md): Computes statistics on genome annotation.
- [Jellyfish](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/jellyfish.md): Counting k-mers in DNA.
- [Kaiju](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/kaiju.md): Taxonomic classification for metagenomics.
- [Kallisto](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/kallisto.md): Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data.
- [K-mer Analysis Toolkit](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/kat.md): Analyses sequencing data via its k-mer spectra.
- [Kraken](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/kraken.md): Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.
- [leeHom](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/leehom.md): Bayesian reconstruction of ancient DNA.
- [Librarian](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/librarian.md): Predicts the sequencing library type from the base composition of a FastQ file.
- [Lima](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/lima.md): Demultiplex PacBio single-molecule sequencing reads.
- [Long Ranger](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/longranger.md): Sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling.
- [MACS2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/macs2.md): Identifies transcription factor binding sites in ChIP-seq data.
- [MALT](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/malt.md): Aligns of metagenomic reads to a database of reference sequences (such as NR, GenBank or Silva) and outputs a MEGAN RMA file.
- [mapDamage](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mapdamage.md): Tracks and quantifies damage patterns in ancient DNA sequences.
- [MEGAHIT](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/megahit.md): NGS read assembler.
- [MetaPhlAn](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/metaphlan.md): Profiles the composition of microbial communities from metagenomic shotgun sequencing data.
- [Methurator](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/methurator.md): Estimates sequencing saturation for reduced-representation bisulfite sequencing (RRBS) data.
- [methylQA](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/methylqa.md): Methylation sequencing data quality assessment tool.
- [mgikit](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mgikit.md): Demultiplexes FASTQ files from an MGI sequencing instrument.
- [MinIONQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/minionqc.md): Quality control for ONT (Oxford Nanopore) long reads.
- [mirtop](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mirtop.md): Annotates miRNAs and isomiRs and compute general statistics in mirGFF3 format.
- [miRTrace](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mirtrace.md): Quality control for small RNA sequencing data.
- [MosaiCatcher](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mosaicatcher.md): Counts strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.
- [Mosdepth](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mosdepth.md): Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
- [Motus](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/motus.md): Microbial profiling through marker gene (MG)-based operational taxonomic units (mOTUs).
- [mtnucratio](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/mtnucratio.md): Computes mitochondrial to nuclear genome ratios in NGS datasets.
- [MultiVCFAnalyzer](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/multivcfanalyzer.md): Reads multiple VCF files into combined genotype calls, produces summary statistics and downstream formats.
- [nanoq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/nanoq.md): Reports read quality and length from nanopore sequencing data.
- [NanoStat](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/nanostat.md): Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).
- [Nextclade](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/nextclade.md): Viral genome alignment, clade assignment, mutation calling, and quality checks.
- [ngs-bits](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ngsbits.md): Calculating statistics from FASTQ, BAM, and VCF.
- [ngsderive](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ngsderive.md): Forensic tool for by backwards computing library information in sequencing data.
- [Nonpareil](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/nonpareil.md): Estimates metagenomic coverage and sequence diversity.
- [ODGI](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/odgi.md): Analysis and manipulation of pangenome graphs structured in the variation graph model.
- [OptiType](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/optitype.md): Precision HLA typing from next-generation sequencing data.
- [pairtools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/pairtools.md): Toolkit for Chromatin Conformation Capture experiments. Handles short-reads paired reference alignments, extracts 3C-specific information, and perf...
- [Pangolin](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/pangolin.md): Uses variant calls to assign SARS-CoV-2 genome sequences to global lineages.
- [pbmarkdup](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/pbmarkdup.md): Takes one or multiple sequencing chips of an amplified libray as HiFi reads and marks or removes duplicates.
- [Peddy](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/peddy.md): Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF.
- [Percolator](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/percolator.md): Semi-supervised learning for peptide identification from shotgun proteomics datasets.
- [phantompeakqualtools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/phantompeakqualtools.md): Computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.
- [Picard](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/picard.md): Tools for manipulating high-throughput sequencing data.
- [Porechop](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/porechop.md): Finds and removes adapters from Oxford Nanopore reads.
- [Preseq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/preseq.md): Estimates library complexity, showing how many additional unique reads are sequenced for increasing total read count.
- [PRINSEQ++](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/prinseqplusplus.md): C++ implementation of the prinseq-lite.pl program. Filters, reformats, and trims genomic and metagenomic reads.
- [Prokka](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/prokka.md): Rapid annotation of prokaryotic genomes.
- [PURPLE](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/purple.md): A purity, ploidy and copy number estimator for whole genome tumor data.
- [Pychopper](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/pychopper.md): Identifies, orients, trims and rescues full length Nanopore cDNA reads. Can also rescue fused reads.
- [pycoQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/pycoqc.md): Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.
- [qc3C](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/qc3C.md): Reference-free and BAM based quality control for Hi-C data.
- [QoRTs](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/qorts.md): Toolkit for analysis, QC, and data management of RNA-Seq datasets.
- [QualiMap](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/qualimap.md): Quality control of alignment data and its derivatives like feature counts.
- [QUAST](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/quast.md): Quality assessment tool for genome assemblies.
- [Ribo-TISH](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ribotish.md): Identifies translated ORFs from Ribo-seq data and reports reading frame quality metrics.
- [riboWaltz](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/ribowaltz.md): Computes P-site offsets and performs quality control for ribosome profiling data.
- [Riker](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/riker.md): Fast Rust toolkit that ports key sequencing QC tools from Picard.
- [RNA-SeQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/rna_seqc.md): RNA-Seq metrics for quality control and process optimization.
- [Rockhopper](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/rockhopper.md): Bacterial RNA-seq analysis: align reads to coding sequences, rRNAs, tRNAs, and miscellaneous RNAs.
- [RSEM](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/rsem.md): Estimates gene and isoform expression levels from RNA-Seq data.
- [RSeQC](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/rseqc.md): Evaluates high throughput RNA-seq data.
- [Salmon](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/salmon.md): Quantifies expression of transcripts using RNA-seq data.
- [Sambamba](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sambamba.md): Toolkit for interacting with BAM/CRAM files.
- [Samblaster](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/samblaster.md): Marks duplicates and extracts discordant and split reads from sam files.
- [Samtools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/samtools.md): Toolkit for interacting with BAM/CRAM files.
- [Sargasso](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sargasso.md): Separates mixed-species RNA-seq reads according to their species of origin.
- [Seqera Platform CLI](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/seqera_cli.md): Reports statistics generated by the Seqera Platform CLI.
- [Seqfu](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/seqfu.md): Manipulate FASTA/FASTQ files.
- [SeqKit](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/seqkit.md): Cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
- [Sequali](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sequali.md): Sequencing quality control for both long-read and short-read data.
- [SeqWho](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/seqwho.md): Determines FASTQ(A) sequencing file source protocol and the species of origin, to check that the composition of the library is expected.
- [SeqyClean](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/seqyclean.md): Filters adapters, vectors, and contaminants while quality trimming.
- [SexDetErrmine](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sexdeterrmine.md): Calculates relative coverage of X and Y chromosomes and their associated error bars from the depth of coverage at specified SNPs.
- [Sickle](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sickle.md): A windowed adaptive trimming tool for FASTQ files using quality.
- [sincei](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sincei.md): Toolkit for processing and analyzing single-cell (epi)genomics data.
- [Skewer](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/skewer.md): Adapter trimming tool for NGS paired-end sequences.
- [Slamdunk](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/slamdunk.md): Tool to analyze SLAM-Seq data.
- [Snippy](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/snippy.md): Rapid haploid variant calling and core genome alignment.
- [SnpEff](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/snpeff.md): Annotates and predicts the effects of variants on genes (such as amino acid changes).
- [SNPsplit](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/snpsplit.md): Allele-specific alignment sorter. Determines allelic origin of reads that cover known SNP positions.
- [Somalier](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/somalier.md): Genotype to pedigree correspondence checks from sketches derived from BAM/CRAM or VCF.
- [som.py](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sompy.md): Benchmarks somatic variant calls against gold standard truth datasets.
- [SortMeRNA](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sortmerna.md): Program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.
- [Sourmash](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sourmash.md): Quickly searches, compares, and analyzes genomic and metagenomic data sets.
- [Space Ranger](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/spaceranger.md): Tool to analyze 10x Genomics spatial transcriptomics data.
- [Stacks](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/stacks.md): Analyzes restriction enzyme-based data (e.g. RAD-seq).
- [STAR](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/star.md): Universal RNA-seq aligner.
- [Supernova](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/supernova.md): De novo genome assembler of 10X Genomics linked-reads.
- [Sylph-tax](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/sylphtax.md): Taxonomic profiling of metagenomic reads.
- [telseq](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/telseq.md): Estimates telomere length from whole genome sequencing data (BAMs).
- [THetA2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/theta2.md): Estimates tumour purity and clonal / subclonal copy number.
- [Tophat](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/tophat.md): Splice junction RNA-Seq reads mapper for mammalian-sized genomes.
- [Trim Galore](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/trim_galore.md): Quality and adapter trimming for next-generation sequencing data, with special handling for RRBS libraries.
- [Trimmomatic](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/trimmomatic.md): Read trimming tool for Illumina NGS data.
- [Truvari](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/truvari.md): Benchmarking, merging, and annotating structural variants.
- [UMICollapse](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/umicollapse.md): Algorithms for efficiently collapsing reads with Unique Molecular Identifiers.
- [UMI-tools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/umitools.md): Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes.
- [VarScan2](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/varscan2.md): Variant detection in massively parallel sequencing data.
- [VCFTools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/vcftools.md): Program to analyse and reporting on VCF files.
- [VEP](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/vep.md): Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.
- [VerifyBAMID](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/verifybamid.md): Detects sample contamination and/or sample swaps.
- [VG](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/vg.md): Toolkit to manipulate and analyze graphical genomes, including read alignment.
- [WhatsHap](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/whatshap.md): Phasing genomic variants using DNA reads (aka read-based phasing, or haplotype assembly).
- [Xengsort](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/xengsort.md): Fast xenograft read sorter based on space-efficient k-mer hashing.
- [Xenium](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/xenium.md): Spatial transcriptomics platform from 10x Genomics that provides subcellular resolution.
- [Xenome](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules/xenome.md): Classifies reads from xenograft sources.
- [Supported Tools](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/modules.md): Tools supported by MultiQC
- [Customising reports](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/reports/customisation.md): Making MultiQC reports bespoke for your use case
- [Using reports](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/reports/reports.md): Getting to grips with MultiQC reports
- [Downstream analysis](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/usage/downstream.md): How to use MultiQC raw data outputs
- [Using MultiQC in pipelines](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/usage/pipelines.md): Integration within your workflow manager of choice
- [Using MultiQC in scripts](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/usage/scripts.md): Importing MultiQC as a library in scripts and notebooks
- [Common problems](https://docs.seqera.io//multiqc_docs/multiqc_repo/docs/markdown/usage/troubleshooting.md): Troubleshooting difficulties

# Fusion

> Documentation for Fusion.

This file contains links to Fusion documentation following the llmstxt.org standard.

## Table of Contents

- [Frequently asked questions](https://docs.seqera.io//fusion_docs/faq.md): Fusion supports AWS S3, Azure Blob, and Google Cloud Storage. Fusion can also be used with local storage solutions that support the AWS S3 API.
- [Get started](https://docs.seqera.io//fusion_docs/get-started.md): Use the Fusion v2 file system in Seqera Platform and Nextflow
- [AWS Batch](https://docs.seqera.io//fusion_docs/guide/aws-batch.md): Use Fusion with AWS Batch and S3 storage
- [Amazon EKS](https://docs.seqera.io//fusion_docs/guide/aws-eks.md): Use Fusion with AWS Elastic Kubernetes Service and S3 storage
- [Azure Batch](https://docs.seqera.io//fusion_docs/guide/azure-batch.md): Use Fusion with Azure Batch and Azure Blob storage
- [Google Cloud Batch](https://docs.seqera.io//fusion_docs/guide/gcp-batch.md): Use Fusion with Google Cloud Batch and Google Cloud Storage
- [Google Kubernetes Engine](https://docs.seqera.io//fusion_docs/guide/gcp-gke.md): Use Fusion with Google Kubernetes Engine and Google Cloud Storage
- [AWS S3](https://docs.seqera.io//fusion_docs/guide/local/aws-s3.md): Use Fusion with the Nextflow local executor and AWS S3
- [Azure Blob Storage](https://docs.seqera.io//fusion_docs/guide/local/azure-blob.md): Use Fusion with the Nextflow local executor and Azure Blob Storage
- [Google Cloud Storage](https://docs.seqera.io//fusion_docs/guide/local/google-cloud.md): Use Fusion with the Nextflow local executor and Google Cloud Storage
- [MinIO](https://docs.seqera.io//fusion_docs/guide/local/minio.md): Use Fusion with the Nextflow local executor and MinIO
- [Oracle Object Storage](https://docs.seqera.io//fusion_docs/guide/local/oracle-object.md): Use Fusion with the Nextflow local executor and Oracle Object Storage
- [AWS Batch](https://docs.seqera.io//fusion_docs/guide/snapshots/aws.md): Fusion Snapshots configuration and best practices for AWS Batch
- [Advanced configuration](https://docs.seqera.io//fusion_docs/guide/snapshots/configuration.md): Advanced configuration options for Fusion Snapshots
- [Google Cloud Batch](https://docs.seqera.io//fusion_docs/guide/snapshots/gcp.md): Fusion Snapshots configuration and best practices for Google Cloud Batch
- [Fusion Snapshots](https://docs.seqera.io//fusion_docs/guide/snapshots/index.md): Introduction to Fusion Snapshots checkpoint/restore functionality
- [User guide](https://docs.seqera.io//fusion_docs/guide.md): Overview of the Fusion v2 file system
- [Fusion file system](https://docs.seqera.io//fusion_docs/index.md): Overview of the Fusion v2 file system
- [Fusion licensing](https://docs.seqera.io//fusion_docs/licensing.md): Understand how Fusion licensing works
- [Reference](https://docs.seqera.io//fusion_docs/reference.md): Fusion configuration options
- [Error codes and exit messages](https://docs.seqera.io//fusion_docs/troubleshooting/error-codes-exit-messages.md): Reference for Fusion error codes, exit codes, and error messages
- [Fusion Doctor](https://docs.seqera.io//fusion_docs/troubleshooting/fusion-doctor.md): Run Fusion Doctor diagnostics with nf-canary to validate Fusion compute environments
- [Fusion Snapshots](https://docs.seqera.io//fusion_docs/troubleshooting/fusion-snapshots.md): Troubleshooting for Fusion Snapshots
- [General](https://docs.seqera.io//fusion_docs/troubleshooting/general.md): Troubleshooting for general Fusion issues

# Wave

> Documentation for Wave.

This file contains links to Wave documentation following the llmstxt.org standard.

## Table of Contents

- [Wave API](https://docs.seqera.io//wave_docs/wave_repo/docs/api.md): This page summarizes the API provided by the Wave container service.
- [Configuration](https://docs.seqera.io//wave_docs/wave_repo/docs/cli/configuration.md): Configure the Wave CLI.
- [Wave CLI](https://docs.seqera.io//wave_docs/wave_repo/docs/cli/index.md): A command-line interface for Wave's container provisioning capabilities.
- [Installation](https://docs.seqera.io//wave_docs/wave_repo/docs/cli/installation.md): Install the Wave CLI from a self-install package or Homebrew.
- [Use cases](https://docs.seqera.io//wave_docs/wave_repo/docs/cli/use-cases.md): Build Docker and Singularity containers from Dockerfiles, Conda packages, and other recipes with the Wave CLI
- [Configuration reference](https://docs.seqera.io//wave_docs/wave_repo/docs/configuration.md): This page documents configuration options for self-hosted Wave deployments.
- [Configure Wave](https://docs.seqera.io//wave_docs/wave_repo/docs/configure-wave.md): This page describes common operations to set up and configure Wave.
- [Frequently asked questions](https://docs.seqera.io//wave_docs/wave_repo/docs/faq.md): Find answers to common questions about Wave container provisioning
- [Container augmentation](https://docs.seqera.io//wave_docs/wave_repo/docs/features/augmentation.md): Inject custom layers into existing container images at pull time, without a rebuild.
- [Private registry authentication](https://docs.seqera.io//wave_docs/wave_repo/docs/features/authentication.md): Access private container registries through Wave using credentials managed in Seqera Platform.
- [On-demand container builds](https://docs.seqera.io//wave_docs/wave_repo/docs/features/container-builds.md): Build container images just-in-time from a Dockerfile, Singularity recipe, Conda environment, Conda lock file, or list of PyPI or CRAN packages.
- [Container freeze](https://docs.seqera.io//wave_docs/wave_repo/docs/features/container-freezes.md): Build a permanent container image and push it to a registry of your choice.
- [Features](https://docs.seqera.io//wave_docs/wave_repo/docs/features/index.md): An overview of Wave's features and deployment configurations.
- [Container inspection](https://docs.seqera.io//wave_docs/wave_repo/docs/features/inspection.md): Retrieve manifest, config, and layer metadata for a container without pulling the image.
- [Container mirroring](https://docs.seqera.io//wave_docs/wave_repo/docs/features/mirroring.md): Copy a container image to a registry of your choice while preserving its original name and digest.
- [Security scanning](https://docs.seqera.io//wave_docs/wave_repo/docs/features/security.md): Scan container images for known vulnerabilities with Trivy and generate SBOMs.
- [Bundling pipeline scripts](https://docs.seqera.io//wave_docs/wave_repo/docs/guides/bundle-scripts.md): Learn how Wave bundles scripts from Nextflow pipelines into container images
- [Reducing Wave API calls](https://docs.seqera.io//wave_docs/wave_repo/docs/guides/reduce-api-calls.md): Learn how to configure Nextflow to freeze containers and reduce API calls
- [How Wave works](https://docs.seqera.io//wave_docs/wave_repo/docs/how-wave-works.md): How Wave provisions and serves container images on demand.
- [Wave](https://docs.seqera.io//wave_docs/wave_repo/docs/index.md): Wave is a container provisioning service. It builds, augments, and serves container images on demand. Pipelines declare their dependencies. Wave re...
- [Configure Wave build](https://docs.seqera.io//wave_docs/wave_repo/docs/install/configure-wave-build.md): This guide covers extending your existing Wave installation on Kubernetes to support container build capabilities. This enables Wave's full feature...
- [Docker Compose installation](https://docs.seqera.io//wave_docs/wave_repo/docs/install/docker-compose.md): Wave enables you to provision container images on demand, removing the need to build and upload them manually to a container registry. Wave can pro...
- [Kubernetes installation](https://docs.seqera.io//wave_docs/wave_repo/docs/install/kubernetes.md): Wave enables you to provision container images on-demand, removing the need to build and upload them manually to a container registry. Wave can can...
- [Migrating to 1.21.0](https://docs.seqera.io//wave_docs/wave_repo/docs/migrations/1-21-0.md): Wave 1.21.0 was released on May 29, 2025.
- [Migrating to 1.24.0](https://docs.seqera.io//wave_docs/wave_repo/docs/migrations/1-24-0.md): Wave 1.24.0 was released on August 12, 2025.
- [Migrating to 1.25.0](https://docs.seqera.io//wave_docs/wave_repo/docs/migrations/1-25-0.md): Wave 1.25.0 was released on September 2, 2025.
- [Migration notes](https://docs.seqera.io//wave_docs/wave_repo/docs/migrations/index.md): This section covers mandatory steps for migrating to new versions of Wave.
- [Configuration reference](https://docs.seqera.io//wave_docs/wave_repo/docs/nextflow/configuration.md): Wave configuration variables for customizing behavior in Nextflow pipelines
- [Nextflow and Wave](https://docs.seqera.io//wave_docs/wave_repo/docs/nextflow/index.md): Learn about integrating Wave with Nextflow
- [Use cases](https://docs.seqera.io//wave_docs/wave_repo/docs/nextflow/use-cases.md): Use Wave with Nextflow to build, provision, and scan pipeline containers
- [Container provisioning](https://docs.seqera.io//wave_docs/wave_repo/docs/provisioning.md): In the container lifecycle, images are generally created (*built*) and uploaded (*pushed*) to a container registry, and then these images are downl...
- [Seqera Containers](https://docs.seqera.io//wave_docs/wave_repo/docs/seqera-containers.md): A free community registry powered by Wave for building Conda and PyPI container images on demand.
- [Troubleshoot](https://docs.seqera.io//wave_docs/wave_repo/docs/troubleshoot.md): 1. How to troubleshoot container build failure?
- [Tutorials](https://docs.seqera.io//wave_docs/wave_repo/docs/tutorials/index.md): Learn how to get started with Wave
- [Nextflow and Seqera Containers](https://docs.seqera.io//wave_docs/wave_repo/docs/tutorials/nextflow-seqera-containers.md): Provision containers with Seqera Containers
- [Nextflow and Wave](https://docs.seqera.io//wave_docs/wave_repo/docs/tutorials/nextflow-wave.md): Provision containers with Nextflow
- [Wave CLI](https://docs.seqera.io//wave_docs/wave_repo/docs/tutorials/wave-cli.md): Provision containers with the Wave CLI

# Nextflow

> Documentation for Nextflow.

This file contains links to Nextflow documentation following the llmstxt.org standard.

## Table of Contents

- [Nextflow documentation](https://docs.seqera.io//docs/README.md): This directory holds the Nextflow documentation content as `.mdx` files. The site is built with [Docusaurus](https://docusaurus.io/) and deployed t...
- [Amazon S3](https://docs.seqera.io//docs/amazons3.md): Use Amazon S3 buckets as a file system in Nextflow pipelines.
- [Amazon Web Services](https://docs.seqera.io//docs/aws.md): Configure and run Nextflow pipelines on AWS.
- [Azure](https://docs.seqera.io//docs/azure.md): Configure and run Nextflow pipelines on Microsoft Azure.
- [Caching and resuming](https://docs.seqera.io//docs/cache-and-resume.md): Cache task executions and resume pipelines using the -resume flag.
- [Command line interface](https://docs.seqera.io//docs/cli.md): Use the Nextflow CLI to manage and execute pipelines from local files or remote repositories.
- [Conda environments](https://docs.seqera.io//docs/conda.md): Use Conda and Bioconda to manage software dependencies.
- [Configuration](https://docs.seqera.io//docs/config.md): Configure Nextflow pipelines using configuration files, scopes, profiles, and environment variables.
- [Containers](https://docs.seqera.io//docs/container.md): Use Docker, Singularity, Apptainer, and other container runtimes with Nextflow.
- [Configuration scopes](https://docs.seqera.io//docs/developer/config-scopes.md): This page provides guidance on defining configuration scopes in the Nextflow runtime.
- [Workflow diagram](https://docs.seqera.io//docs/developer/diagram.md): The following diagram is a high-level overview of the Nextflow source code in a similar style as the [workflow diagram][workflow-diagram] visualiza...
- [Class Diagrams](https://docs.seqera.io//docs/developer/diagrams/README.md): This directory contains class diagrams of the Nextflow source code, abridged and annotated for relevance and ease of use.
- [Overview](https://docs.seqera.io//docs/developer/index.md): This section provides a high-level overview of the Nextflow source code for users who want to understand or contribute to it. Rather than a compreh...
- [`nextflow.ast`](https://docs.seqera.io//docs/developer/nextflow.ast.md): The `nextflow.ast` package implements the Nextflow language extensions as AST transforms.
- [`nextflow.cache`](https://docs.seqera.io//docs/developer/nextflow.cache.md): The `nextflow.cache` package implements the cache database of previously executed tasks.
- [`nextflow.cli`](https://docs.seqera.io//docs/developer/nextflow.cli.md): The `nextflow.cli` package implements the command line interface.
- [`nextflow.cloud.aws`](https://docs.seqera.io//docs/developer/nextflow.cloud.aws.md): The `nextflow.cloud.aws` package implements the AWS Batch executor.
- [`nextflow.cloud.aws.nio`](https://docs.seqera.io//docs/developer/nextflow.cloud.aws.nio.md): The `nextflow.cloud.aws.nio` package implements the S3 filesystem.
- [`nextflow.cloud.azure`](https://docs.seqera.io//docs/developer/nextflow.cloud.azure.md): The `nextflow.cloud.azure` package implements the Azure Batch executor.
- [`nextflow.cloud.google`](https://docs.seqera.io//docs/developer/nextflow.cloud.google.md): The `nextflow.cloud.google` package implements the Google Batch executor.
- [`nextflow.config`](https://docs.seqera.io//docs/developer/nextflow.config.md): The `nextflow.config` package contains the implementation of the Nextflow configuration.
- [`nextflow.container`](https://docs.seqera.io//docs/developer/nextflow.container.md): The `nextflow.container` package implements the integration with container runtimes.
- [`nextflow.dag`](https://docs.seqera.io//docs/developer/nextflow.dag.md): The `nextflow.dag` package implements the workflow DAG and renderers for several diagram formats.
- [`nextflow.executor`](https://docs.seqera.io//docs/developer/nextflow.executor.md): The `nextflow.executor` package defines the executor interface and implements several built-in executors.
- [`nextflow.extension`](https://docs.seqera.io//docs/developer/nextflow.extension.md): The `nextflow.extension` package implements the channel operators and other extension methods.
- [`nextflow.k8s`](https://docs.seqera.io//docs/developer/nextflow.k8s.md): The `nextflow.k8s` package implements the Kubernetes executor and the `kuberun` command.
- [`nextflow`](https://docs.seqera.io//docs/developer/nextflow.md): The `nextflow` package contains various top-level classes.
- [`nextflow.plugin`](https://docs.seqera.io//docs/developer/nextflow.plugin.md): The `nextflow.plugin` package implements the plugin manager.
- [`nextflow.processor`](https://docs.seqera.io//docs/developer/nextflow.processor.md): The `nextflow.processor` package implements the execution and monitoring of tasks.
- [`nextflow.scm`](https://docs.seqera.io//docs/developer/nextflow.scm.md): The `nextflow.scm` package defines the Git provider interface and implements several built-in Git providers. It also manages local pipeline reposit...
- [`nextflow.script`](https://docs.seqera.io//docs/developer/nextflow.script.md): The `nextflow.script` package implements the parsing and execution of Nextflow scripts.
- [`nextflow.secret`](https://docs.seqera.io//docs/developer/nextflow.secret.md): The `nextflow.secret` package defines the secrets provider interface and implements the built-in local secrets store.
- [`nextflow.trace`](https://docs.seqera.io//docs/developer/nextflow.trace.md): The `nextflow.trace` package defines the trace observer interface and implements several built-in trace observers.
- [Packages](https://docs.seqera.io//docs/developer/packages.md): import DocCardList from "@theme/DocCardList";
- [Environment setup](https://docs.seqera.io//docs/developer-env.md): Set up a Nextflow development environment.
- [Executors](https://docs.seqera.io//docs/executor.md): Configure Nextflow executors to run pipeline processes on local machines, HPC schedulers, and cloud platforms.
- [Fusion file system](https://docs.seqera.io//docs/fusion.md): Use the Fusion virtual file system to enable fast, POSIX-compatible access to cloud object stores.
- [Git integration](https://docs.seqera.io//docs/git.md): Configure Nextflow's Git integration for accessing private repositories.
- [Google Cloud](https://docs.seqera.io//docs/google.md): Configure and run Nextflow pipelines on Google Cloud.
- [AWS Java SDK v2](https://docs.seqera.io//docs/guides/aws-java-sdk-v2.md): Migrate your Nextflow AWS configuration to use AWS Java SDK v2.
- [Using the Nextflow Gradle plugin](https://docs.seqera.io//docs/guides/gradle-plugin.md): Use the Nextflow Gradle plugin to build, test, and publish Nextflow plugins.
- [Migrating to the Nextflow plugin registry](https://docs.seqera.io//docs/guides/migrate-plugin.md): Migrate Nextflow plugins from the legacy plugin index to the Nextflow plugin registry.
- [Spot Instance failures and retries](https://docs.seqera.io//docs/guides/updating-spot-retries.md): Configure Nextflow to handle Spot Instance failures and retries.
- [Nextflow](https://docs.seqera.io//docs/index.md): Create scalable, portable, and reproducible workflows using Nextflow's dataflow programming model.
- [Installation](https://docs.seqera.io//docs/install.md): Install Nextflow on Linux, macOS, and Windows using the self-installing package, Conda, or a standalone distribution.
- [Kubernetes](https://docs.seqera.io//docs/kubernetes.md): Deploy and run Nextflow pipelines on Kubernetes clusters.
- [Migrating to 24.04](https://docs.seqera.io//docs/migrations/24-04.md): Review new features, breaking changes, and deprecations introduced in Nextflow 24.04.
- [Migrating to 24.10](https://docs.seqera.io//docs/migrations/24-10.md): Review new features, breaking changes, and deprecations introduced in Nextflow 24.10.
- [Migrating to 25.04](https://docs.seqera.io//docs/migrations/25-04.md): Review new features, breaking changes, and deprecations introduced in Nextflow 25.04.
- [Migrating to 25.10](https://docs.seqera.io//docs/migrations/25-10.md): Review new features, breaking changes, and deprecations introduced in Nextflow 25.10.
- [Migrating to 26.04](https://docs.seqera.io//docs/migrations/26-04.md): Review new features, breaking changes, and deprecations introduced in Nextflow 26.04.
- [Migrating from DSL1](https://docs.seqera.io//docs/migrations/dsl1.md): Migrate Nextflow pipelines from DSL1 to DSL2.
- [Migration notes](https://docs.seqera.io//docs/migrations/index.md): Find important information for migrating between Nextflow versions.
- [Developing modules](https://docs.seqera.io//docs/modules/developing-modules.md): Create modules and share them through the Nextflow module registry.
- [Nextflow module registry](https://docs.seqera.io//docs/modules/module-registry.md): Use the Nextflow module registry to discover, share, track, and verify modules.
- [Overview](https://docs.seqera.io//docs/modules/modules.md): Reuse Nextflow definitions across pipelines using local and registry modules.
- [Using modules](https://docs.seqera.io//docs/modules/using-modules.md): Discover, install, and run Nextflow modules from the module registry.
- [Notifications](https://docs.seqera.io//docs/notifications.md): Handle workflow completion and error events and send email notifications.
- [Overview](https://docs.seqera.io//docs/overview.md): Understand Nextflow's core concepts, including processes, dataflow, execution abstraction, and configuration.
- [Developing plugins](https://docs.seqera.io//docs/plugins/developing-plugins.md): Create, build, test, and publish Nextflow plugins using the plugin template and Gradle build tools.
- [Nextflow plugin registry](https://docs.seqera.io//docs/plugins/plugin-registry.md): Use the Nextflow plugin registry to discover, publish, and manage Nextflow plugins.
- [Plugins](https://docs.seqera.io//docs/plugins/plugins.md): Discover and use Nextflow plugins to extend pipeline functionality.
- [Using plugins](https://docs.seqera.io//docs/plugins/using-plugins.md): Configure and use core and third-party Nextflow plugins in your pipelines.
- [Processes (typed)](https://docs.seqera.io//docs/process-typed.md): Use the typed process syntax in Nextflow to define statically typed inputs and outputs for processes.
- [Processes](https://docs.seqera.io//docs/process.md): Define and configure Nextflow processes.
- [Channel factories](https://docs.seqera.io//docs/reference/channel.md): Reference for all Nextflow channel factory methods used to create channels.
- [CLI reference](https://docs.seqera.io//docs/reference/cli.md): Reference for all Nextflow CLI options, commands, and subcommands.
- [Configuration options](https://docs.seqera.io//docs/reference/config.md): Reference for Nextflow configuration settings.
- [Environment variables](https://docs.seqera.io//docs/reference/env-vars.md): Reference for all environment variables that control the Nextflow runtime and JVM.
- [Feature flags](https://docs.seqera.io//docs/reference/feature-flags.md): Reference for feature flags in Nextflow.
- [Operators (typed)](https://docs.seqera.io//docs/reference/operator-typed.md): Reference for the core Nextflow operators recommended for use with static typing.
- [Operators (legacy)](https://docs.seqera.io//docs/reference/operator.md): Reference for legacy Nextflow channel operators.
- [Process reference](https://docs.seqera.io//docs/reference/process.md): Reference for all task properties, input and output qualifiers, and directives available in process definitions.
- [Semantics](https://docs.seqera.io//docs/reference/semantics.md): Reference for the semantics of Nextflow language constructs.
- [Groovy and Java classes](https://docs.seqera.io//docs/reference/stdlib-groovy.md): Reference for Groovy and Java classes available to Nextflow at runtime.
- [Namespaces](https://docs.seqera.io//docs/reference/stdlib-namespaces.md): Reference for namespaces in the Nextflow standard library.
- [Types](https://docs.seqera.io//docs/reference/stdlib-types.md): Reference for the standard types in the Nextflow standard library.
- [Standard library](https://docs.seqera.io//docs/reference/stdlib.md): Reference for the Nextflow standard library.
- [Syntax](https://docs.seqera.io//docs/reference/syntax.md): Reference for the Nextflow language syntax.
- [Reports](https://docs.seqera.io//docs/reports.md): Generate and interpret Nextflow execution reports, timelines, trace files, and workflow diagrams.
- [Scripts](https://docs.seqera.io//docs/script.md): A practical introduction to writing Nextflow scripts with variables, strings, collections, operators, control flow, and closures.
- [Secrets](https://docs.seqera.io//docs/secrets.md): Securely manage and inject sensitive credentials using the built-in secrets store.
- [Sharing pipelines](https://docs.seqera.io//docs/sharing.md): Publish and run Nextflow pipelines using Nextflow's built-in Git integration.
- [Spack environments](https://docs.seqera.io//docs/spack.md): Use Spack to manage software dependencies, including recipes, environment files, and multi-architecture builds.
- [Preparing for strict syntax](https://docs.seqera.io//docs/strict-syntax.md): Update Nextflow scripts and configuration files to comply with the strict Nextflow language specification.
- [Getting started with data lineage](https://docs.seqera.io//docs/tutorials/data-lineage.md): Enable and use Nextflow's data lineage feature.
- [Using Nextflow with Flux](https://docs.seqera.io//docs/tutorials/flux.md): Set up and run Nextflow pipelines using the Flux Framework resource manager.
- [Understanding task resource metrics](https://docs.seqera.io//docs/tutorials/metrics.md): Interpret CPU, memory, and I/O resource usage metrics in Nextflow.
- [Getting started with rnaseq-nf](https://docs.seqera.io//docs/tutorials/rnaseq-nf.md): Follow a step-by-step walkthrough of the rnaseq-nf pipeline.
- [Using operators with static typing](https://docs.seqera.io//docs/tutorials/static-types-operators.md): Best practices for using operators with static typing in Nextflow.
- [Migrating to static typing](https://docs.seqera.io//docs/tutorials/static-types.md): Migrate Nextflow pipelines to static typing using records, type annotations, and typed processes.
- [Migrating to workflow outputs](https://docs.seqera.io//docs/tutorials/workflow-outputs.md): Migrate from the publishDir directive to the workflow output definition.
- [Updating Nextflow](https://docs.seqera.io//docs/updating-nextflow.md): Update, pin, and switch between Nextflow versions.
- [VS Code integration](https://docs.seqera.io//docs/vscode.md): Use the Nextflow VS Code extension for syntax highlighting, diagnostics, code navigation, and other language features.
- [Wave containers](https://docs.seqera.io//docs/wave.md): Use Wave to automatically build and provision container images on demand.
- [Workflows (typed)](https://docs.seqera.io//docs/workflow-typed.md): Use typed workflows in Nextflow to define statically typed inputs and outputs for workflows.
- [Workflows](https://docs.seqera.io//docs/workflow.md): Define entry workflows and named workflows in Nextflow.
- [Working with files](https://docs.seqera.io//docs/working-with-files.md): Read, write, copy, and manage files and directories in Nextflow scripts.
- [Your first script](https://docs.seqera.io//docs/your-first-script.md): Run, modify, and configure your first Nextflow pipeline.