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- Added option to disable printing workflow outputs by @bentsherman in [#7018](https://github.com/nextflow-io/nextflow/pull/7018)
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- Resolved structured process input types by @bentsherman in [#7014](https://github.com/nextflow-io/nextflow/pull/7014)
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### S3
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- Applied socket timeout to S3 CRT connections by @jorgee in [#7024](https://github.com/nextflow-io/nextflow/pull/7024)
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- Managed AWS SDK exceptions to convert to the appropriate IO exceptions by @jorgee in [#6707](https://github.com/nextflow-io/nextflow/pull/6707)
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### Plugins
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- Updated missing `pf4j` updates by @jorgee in [#7016](https://github.com/nextflow-io/nextflow/pull/7016)
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### Fusion
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- Added Fusion GPU metrics collection by @pditommaso in [#7022](https://github.com/nextflow-io/nextflow/pull/7022)
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- Used Fusion trace metrics to replace bash command-trace wrapper by @pditommaso in [#7041](https://github.com/nextflow-io/nextflow/pull/7041)
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### General
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- Added `-files-from` option to `lint` command to avoid `ARG_MAX` limit by @adamrtalbot in [#6858](https://github.com/nextflow-io/nextflow/pull/6858)
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- Added 26.04 migration docs by @bentsherman in [#7000](https://github.com/nextflow-io/nextflow/pull/7000)
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- Allowed cloning from local Git repositories when `--offline` by @MatthiasZepper in [#7035](https://github.com/nextflow-io/nextflow/pull/7035)
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- Allowed running pipeline from URL and main script path by @jorgee in [#6602](https://github.com/nextflow-io/nextflow/pull/6602)
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- Filtered `autoLabels` to selected workflow-metadata fields by @pditommaso in [#7049](https://github.com/nextflow-io/nextflow/pull/7049)
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- Honored `process.resourceLabels` in `nf-seqera` executor by @pditommaso in [#7048](https://github.com/nextflow-io/nextflow/pull/7048)
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- Renamed `module info` subcommand to `module view` by @pditommaso in [#7052](https://github.com/nextflow-io/nextflow/pull/7052)
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- Simplified demo module README template by @pditommaso in [#7051](https://github.com/nextflow-io/nextflow/pull/7051)
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- Suppressed `lint` progress logging with `-q` flag by @ewels in [#6880](https://github.com/nextflow-io/nextflow/pull/6880)
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## Bug fixes
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### Language features
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- Fixed formatting issues with complex expressions by @bentsherman in [#7027](https://github.com/nextflow-io/nextflow/pull/7027)
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### S3
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- Fixed `S3FileSystemProvider.newInputStream()` draining full object on close by @jorgee in [#7046](https://github.com/nextflow-io/nextflow/pull/7046)
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### Plugins
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- Fixed inconsistent indentation in `nf-amazon` by @bentsherman in [#7047](https://github.com/nextflow-io/nextflow/pull/7047)
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- Fixed `nextflowVersion` for `nf-tower` and `nf-seqera` plugins by @pditommaso in [cbc0a2d8e](https://github.com/nextflow-io/nextflow/commit/cbc0a2d8e)
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### General
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- Fixed generated process name in `module create` command by @jorgee in [#7008](https://github.com/nextflow-io/nextflow/pull/7008)
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- Fixed `module info` formatting separator by @pditommaso in [#7033](https://github.com/nextflow-io/nextflow/pull/7033)
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- Fixed resolution of `-with-tower` with `TOWER_API_ENDPOINT` by @bentsherman in [#7045](https://github.com/nextflow-io/nextflow/pull/7045)
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- Fixed `saveCacheFiles` early return skipping log file uploads by @munishchouhan in [#7015](https://github.com/nextflow-io/nextflow/pull/7015)
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## Dependencies
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- Bumped `org.bouncycastle:bcpkix-jdk18on` from 1.79 to 1.84 by @dependabot in [#7042](https://github.com/nextflow-io/nextflow/pull/7042)
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---
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title: "Advanced options"
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description: "Advanced guide to launching Nextflow pipelines in Seqera Platform"
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date: "21 Apr 2023"
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description: "Advanced guide to launching Nextflow pipelines in Seqera Platform."
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date created: "2023-04-21"
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last updated: "2026-04-02"
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tags: [advanced, launch]
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---
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You can modify the configuration and execution of a pipeline with advanced launch options.
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###Nextflow config file
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## Nextflow config file
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Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax).
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Add additional or modified Nextflow configuration settings. Use the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax).
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For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section:
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### Nextflow configuration order of priority
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```ini
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manifest {
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name = 'My_RNASeq_Pipeline'
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description = 'Generates RNASeq results using a test profile'
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}
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```
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When launching pipelines in Platform, Nextflow configuration is resolved from four sources. If the same parameter is defined in more than one source, the highest-priority source is used:
When launching pipelines in Platform, Nextflow configuration values can be supplied from the `nextflow.config` file in the pipeline repository and the **Nextflow config file** field in the pipeline launch form. If different values of the same configuration parameter are defined, Nextflow parameters defined in the launch form **Nextflow config file** field override the same parameters in your `nextflow.config` file.
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Configuration values set in the **Global Nextflow config** field during compute environment creation are pre-filled in the **Nextflow config file** field during pipeline launch. These pre-filled values from the compute environment can be overridden manually during launch.
**Global Nextflow config** values are pre-filled in the launch form's **Nextflow config file** field, but also apply independently at the priority level shown above. Clearing the launch form field does not remove the **Global Nextflow config** values.
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:::
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For example, if:
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1. The `nextflow.config` file in your pipeline repository contains this manifest:
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1. The pipeline repository `nextflow.config` file contains this manifest:
The resolved configuration will contain the **Nextflow config file** field's manifest:
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```ini title="Pipeline launch form Nextflow config file field"
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manifest {
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name = 'C'
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description = 'Pipeline description C'
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}
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```
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```ini title="Resolved configuration"
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manifest {
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name = 'C'
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description = 'Pipeline description C'
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}
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```
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### Platform-managed configuration
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Platform generates a configuration file from the compute environment definition. For any property defined in both this file and the pipeline repository `nextflow.config`, the Platform-generated value takes precedence. There is no warning repository config values are replaced.
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### Pre-launch configuration preview
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The configuration preview shown on the launch form reflects the **Nextflow config file** field and the compute environment's **Global Nextflow config** field only. Platform-managed compute settings and the pipeline repository `nextflow.config` are not visible in the preview. Both are resolved at launch time.
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:::tip{title="Best practices"}
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To ensure compute-specific settings are applied consistently:
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- Define compute-specific settings in the compute environment's **Global Nextflow config** field or the launch form's **Nextflow config file** field to make settings visible in the pre-launch preview and ensure they apply regardless of what the repository config contains.
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- Use the launch form's **Nextflow config file** field for settings that must take precedence over everything else.
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:::
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### Seqera Cloud config file
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## Seqera Cloud config file
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Configure per-pipeline Seqera reporting behavior. Settings specified here override the default configuration for this execution. Use the `reports` key to specify report paths, titles, and MIME types:
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mimeType: "text/html"
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```
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### Pre and post-run scripts
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## Pre and post-run scripts
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Run custom code either before or after the execution of the Nextflow script. These fields allow you to enter shell commands.
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Post-run script failures do not affect the workflow exit status. Post-run scripts have a maximum size limit of 1 KB.
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:::
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### Stub run
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## Stub run
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Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution.
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### Main script
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## Main script
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Nextflow will attempt to run the script named `main.nf` in the root of the project repository by default. You can configure a custom script path and/or filename in `manifest.mainScript`, or you can provide the script path and filename in this field.
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If you specify a custom script filename, the root of the default branch in your pipeline repository must still contain a `main.nf` file, even if blank. See [Nextflow configuration](../troubleshooting_and_faqs/nextflow) for more information on this known Nextflow behavior.
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:::
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### Workflow entry name
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## Workflow entry name
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Nextflow DSL2 provides the ability to launch workflows with specific names. Enter the name of the workflow to be executed in this field.
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### Schema name
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## Schema name
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Specify the name of a pipeline schema file in the workflow repository root folder to override the default `nextflow_schema.json`.
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### Head job CPUs and memory
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## Head job CPUs and memory
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Specify the compute resources allocated to the Nextflow head job. These fields are only displayed for runs executing on [AWS Batch](../compute-envs/aws-batch) and [Azure Batch](../compute-envs/azure-batch) compute environments.
Copy file name to clipboardExpand all lines: platform-enterprise_docs/launch/advanced.md
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title: "Advanced options"
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description: "Advanced guide to launching Nextflow pipelines in Seqera Platform."
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date created: "2023-04-21"
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last updated: "2025-12-12"
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last updated: "2026-04-02"
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tags: [advanced, launch]
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---
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You can modify the configuration and execution of a pipeline with advanced launch options.
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###Nextflow config file
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## Nextflow config file
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Add settings to the Nextflow configuration file. This must follow the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax).
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Add additional or modified Nextflow configuration settings. Use the same syntax as the [Nextflow configuration file](https://docs.seqera.io/nextflow/config#config-syntax).
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For example, modify the **manifest** section to give the pipeline a name and description that will show up in the Seqera monitoring section:
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### Nextflow configuration order of priority
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```ini
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manifest {
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name = 'My_RNASeq_Pipeline'
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description = 'Generates RNASeq results using a test profile'
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}
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```
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When launching pipelines in Platform, Nextflow configuration is resolved from four sources. If the same parameter is defined in more than one source, the highest-priority source is used:
When launching pipelines in Platform, Nextflow configuration values can be supplied from the `nextflow.config` file in the pipeline repository and the **Nextflow config file** field in the pipeline launch form. If different values of the same configuration parameter are defined, Nextflow parameters defined in the launch form **Nextflow config file** field override the same parameters in your `nextflow.config` file.
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Configuration values set in the **Global Nextflow config** field during compute environment creation are pre-filled in the **Nextflow config file** field during pipeline launch. These pre-filled values from the compute environment can be overridden manually during launch.
**Global Nextflow config** values are pre-filled in the launch form's **Nextflow config file** field, but also apply independently at the priority level shown above. Clearing the launch form field does not remove the **Global Nextflow config** values.
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:::
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For example, if:
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1. The `nextflow.config` file in your pipeline repository contains this manifest:
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1. The pipeline repository `nextflow.config` file contains this manifest:
The resolved configuration will contain the **Nextflow config file** field's manifest:
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```ini title="Pipeline launch form Nextflow config file field"
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manifest {
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name = 'C'
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description = 'Pipeline description C'
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}
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```
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```ini title="Resolved configuration"
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manifest {
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name = 'C'
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description = 'Pipeline description C'
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}
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```
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### Platform-managed configuration
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Platform generates a configuration file from the compute environment definition. For any property defined in both this file and the pipeline repository `nextflow.config`, the Platform-generated value takes precedence. There is no warning repository config values are replaced.
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### Pre-launch configuration preview
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The configuration preview shown on the launch form reflects the **Nextflow config file** field and the compute environment's **Global Nextflow config** field only. Platform-managed compute settings and the pipeline repository `nextflow.config` are not visible in the preview. Both are resolved at launch time.
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:::tip{title="Best practices"}
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To ensure compute-specific settings are applied consistently:
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- Define compute-specific settings in the compute environment's **Global Nextflow config** field or the launch form's **Nextflow config file** field to make settings visible in the pre-launch preview and ensure they apply regardless of what the repository config contains.
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- Use the launch form's **Nextflow config file** field for settings that must take precedence over everything else.
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:::
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### Seqera Cloud config file
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## Seqera Cloud config file
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Configure per-pipeline Seqera reporting behavior. Settings specified here override the same settings in the `tower.yml` [configuration file](../enterprise/configuration/overview) for this execution. Use the `reports` key to specify report paths, titles, and MIME types:
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mimeType: "text/html"
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```
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### Pre and post-run scripts
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## Pre and post-run scripts
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Run custom code either before or after the execution of the Nextflow script. These fields allow you to enter shell commands.
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Post-run script failures do not affect the workflow exit status. Post-run scripts have a maximum size limit of 1 KB.
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:::
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### Pull latest
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## Pull latest
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Instruct Nextflow to pull the latest pipeline version from the Git repository. This is equivalent to using the `-latest` flag.
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Instruct Nextflow to pull the latest pipeline version from the pipeline repository. This is equivalent to using the `-latest` flag.
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### Stub run
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## Stub run
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Replace Nextflow process commands with command [stubs](https://docs.seqera.io/nextflow/process#stub), where defined, before execution.
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### Main script
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## Main script
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Nextflow will attempt to run the script named `main.nf` in the root of the project repository by default. You can configure a custom script path and/or filename in `manifest.mainScript`, or you can provide the script path and filename in this field.
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If you specify a custom script filename, the root of the default branch in your pipeline repository must still contain a `main.nf` file, even if blank. See [Nextflow configuration](../troubleshooting_and_faqs/nextflow) for more information on this known Nextflow behavior.
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:::
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### Workflow entry name
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## Workflow entry name
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Nextflow DSL2 provides the ability to launch workflows with specific names. Enter the name of the workflow to be executed in this field.
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### Schema name
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## Schema name
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Specify the name of a pipeline schema file in the workflow repository root folder to override the default `nextflow_schema.json`.
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### Head job CPUs and memory
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## Head job CPUs and memory
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Specify the compute resources allocated to the Nextflow head job. These fields are only displayed for runs executing on [AWS Batch](../compute-envs/aws-batch) and [Azure Batch](../compute-envs/azure-batch) compute environments.
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