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README.md
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README.md
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A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
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## Table of contents
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* [Using an existing config](#using-an-existing-config)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Adding a new config](#adding-a-new-config)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline Specific Documentation](#pipeline-specific-documentation)
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* [Enabling the specific configs within a specific pipeline](#enabling-the-specific-configs-within-a-specific-pipeline)
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* [Create the specific `nf-core/configs` for the pipeline](#create-the-specific-nf-coreconfigs-for-the-pipeline)
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* [Pipeline Specific Documentation](#pipeline-specific-documentation)
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* [Enabling the specific configs within a specific pipeline](#enabling-the-specific-configs-within-a-specific-pipeline)
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* [Create the specific `nf-core/configs` for the pipeline](#create-the-specific-nf-coreconfigs-for-the-pipeline)
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* [Help](#help)
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## Using an existing config
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The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation.
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The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally.
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However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation.
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### Configuration and parameters
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The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all nf-core pipelines.
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All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customize the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
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All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both.
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For example, if you have the ability to use [Singularity](https://sylabs.io/singularity/) on your HPC you can add and customize the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file.
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Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster.
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In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
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You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf).
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### Offline usage
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If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline with `--custom_config_base`
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or `params.custom_config_base` set to the location of the directory containing the repository files:
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If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline.
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Then run the pipeline with `--custom_config_base` or `params.custom_config_base` set to the location of the directory containing the repository files:
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```bash
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## Download and unzip the config files
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nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
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```
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Alternatively, instead of using the configuration profiles from this repository, you can run your
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pipeline directly calling the single institutional config file that you need with the `-c` parameter.
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Alternatively, instead of using the configuration profiles from this repository, you can run your pipeline directly calling the single institutional config file that you need with the `-c` parameter.
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```bash
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nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
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```
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> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
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> files + singularity containers + institutional configs in one go for you, to make this process easier.
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> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
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## Adding a new config
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If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation.
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You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
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See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.
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Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values.
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Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.
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## Checking user hostnames
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If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile.
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Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name.
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If the user's hostname contains this string at the start of a run or when a run fails and their profile
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does not contain the profile name, a warning message will be printed.
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If the user's hostname contains this string at the start of a run or when a run fails and their profile does not contain the profile name, a warning message will be printed.
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### Testing
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@ -80,7 +85,8 @@ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[pat
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### Documentation
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You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation. You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there.
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You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation.
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You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there.
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See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.
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### Uploading to `nf-core/configs`
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[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
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[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account.
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Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory.
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You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
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You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
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We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
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## Adding a new pipeline specific config
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## Adding a new pipeline-specific config
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Follow the previous guidelines to create a nf-core/configs, update the pipeline specific documentation, and create the necessary files.
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Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines.
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In a similar manner, replace `<PROFILE>` by the name of the profile.
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Here we will be adding an institutional pipeline-specific config.
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:warning: Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines.
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:warning: In a similar manner, replace `<PROFILE>` by the name of the profile.
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Currently the `nextflow.config` file from any pipeline, load the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config), which load the institutional configuration file based on the profile `<PROFILE>`.
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We're adding within the `nextflow.config` from the pipeline `<PIPELINE>`, the loading of the `pipeline/<PIPELINE>.config` from the [`nf-core/configs`](https://github.com/nf-core/configs) repo, which load the `<PIPELINE>` specific institution configuration file based on the profile `<PROFILE>`.
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`nextflow.config` from pipeline will load first institutional configuration file and then the pipeline-specific institutional configuration file.
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Each configuration file will add new params and overwrite the params already existing.
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Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` set to reasonable values.
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Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example.
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### Pipeline specific documentation
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Currently documentation is available for the following pipelines within the specific profile:
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Currently documentation is available for the following pipeline within the specific profile:
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
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If not already present, add to `nextflow.config`
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[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` repository to your own GitHub account.
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Within the local clone of your fork, if not already present, add to `nextflow.config`
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```Groovy
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// Load nf-core/<PIPELINE> custom profiles from different Institutions
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}
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```
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/<PIPELINE>` GitHub repo with the appropriate information.
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We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
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### Create the specific nf-core/configs for the pipeline
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:warning: This has to be done on a fork of the `nf-core/configs` repository.
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If not already created, add the `pipeline/<PIPELINE>.config` file, and add the profile <PROFILE> to the profile scope
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[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account.
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Within the local clone of your fork, if not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
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```Groovy
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profiles {
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}
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```
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Add the `conf/pipeline/<PIPELINE>/<PROFILE>.config` file with all pipeline specific params, `withLabel` or any other configuration profile.
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Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
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Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
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You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
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Add the `docs/pipeline/<PIPELINE>/<PROFILE>.md` file with documentation on what are the specificity of this configs.
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
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## Help
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If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).
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If you have any questions or issues please send us a message on [Slack](https://nfcore.slack.com/channels/configs).
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