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@ -5,35 +5,40 @@
A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
## Table of contents ## Table of contents
* [Using an existing config](#using-an-existing-config) * [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters) * [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage) * [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config) * [Adding a new config](#adding-a-new-config)
* [Testing](#testing) * [Testing](#testing)
* [Documentation](#documentation) * [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline specific config](#adding-a-new-pipeline-specific-config) * [Adding a new pipeline specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline Specific Documentation](#pipeline-specific-documentation) * [Pipeline Specific Documentation](#pipeline-specific-documentation)
* [Enabling the specific configs within a specific pipeline](#enabling-the-specific-configs-within-a-specific-pipeline) * [Enabling the specific configs within a specific pipeline](#enabling-the-specific-configs-within-a-specific-pipeline)
* [Create the specific `nf-core/configs` for the pipeline](#create-the-specific-nf-coreconfigs-for-the-pipeline) * [Create the specific `nf-core/configs` for the pipeline](#create-the-specific-nf-coreconfigs-for-the-pipeline)
* [Help](#help) * [Help](#help)
## Using an existing config ## Using an existing config
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. 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.
### Configuration and parameters ### Configuration and parameters
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. 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.
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. 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://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.
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.
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). 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).
### Offline usage ### Offline usage
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` 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.
or `params.custom_config_base` set to the location of the directory containing the repository files: Then run the pipeline with `--custom_config_base` or `params.custom_config_base` set to the location of the directory containing the repository files:
```bash ```bash
## Download and unzip the config files ## Download and unzip the config files
@ -46,28 +51,28 @@ cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/ nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
``` ```
Alternatively, instead of using the configuration profiles from this repository, you can run your 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.
pipeline directly calling the single institutional config file that you need with the `-c` parameter.
```bash ```bash
nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
``` ```
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline > 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.
> files + singularity containers + institutional configs in one go for you, to make this process easier.
## Adding a new config ## Adding a new config
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. 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.
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. 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.
## Checking user hostnames ## Checking user hostnames
If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile. If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile.
Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name. Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name.
If the user's hostname contains this string at the start of a run or when a run fails and their profile 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.
does not contain the profile name, a warning message will be printed.
### Testing ### Testing
@ -80,7 +85,8 @@ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[pat
### Documentation ### Documentation
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. 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.
See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples. See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.
@ -113,21 +119,35 @@ Currently documentation is available for the following systems:
### Uploading to `nf-core/configs` ### Uploading to `nf-core/configs`
[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. [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.
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.
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. 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.
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. 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.
## Adding a new pipeline specific config ## Adding a new pipeline-specific config
Follow the previous guidelines to create a nf-core/configs, update the pipeline specific documentation, and create the necessary files. Here we will be adding an institutional pipeline-specific config.
Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines.
In a similar manner, replace `<PROFILE>` by the name of the profile. :warning: Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines.
:warning: In a similar manner, replace `<PROFILE>` by the name of the profile.
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>`.
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>`.
`nextflow.config` from pipeline will load first institutional configuration file and then the pipeline-specific institutional configuration file.
Each configuration file will add new params and overwrite the params already existing.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` set to reasonable values.
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.
### Pipeline specific documentation ### Pipeline specific documentation
Currently documentation is available for the following pipelines within the specific profile: Currently documentation is available for the following pipeline within the specific profile:
* sarek * sarek
* [MUNIN](docs/pipeline/sarek/munin.md) * [MUNIN](docs/pipeline/sarek/munin.md)
@ -136,7 +156,8 @@ Currently documentation is available for the following pipelines within the spec
:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.** :warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
If not already present, add to `nextflow.config` [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` repository to your own GitHub account.
Within the local clone of your fork, if not already present, add to `nextflow.config`
```Groovy ```Groovy
// Load nf-core/<PIPELINE> custom profiles from different Institutions // Load nf-core/<PIPELINE> custom profiles from different Institutions
@ -147,11 +168,16 @@ try {
} }
``` ```
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.
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.
### Create the specific nf-core/configs for the pipeline ### Create the specific nf-core/configs for the pipeline
:warning: This has to be done on a fork of the `nf-core/configs` repository. :warning: This has to be done on a fork of the `nf-core/configs` repository.
If not already created, add the `pipeline/<PIPELINE>.config` file, and add the profile <PROFILE> to the profile scope [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, if not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
```Groovy ```Groovy
profiles { profiles {
@ -159,10 +185,12 @@ profiles {
} }
``` ```
Add the `conf/pipeline/<PIPELINE>/<PROFILE>.config` file with all pipeline specific params, `withLabel` or any other configuration profile. Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
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.
Add the `docs/pipeline/<PIPELINE>/<PROFILE>.md` file with documentation on what are the specificity of this configs. 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.
## Help ## Help
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack). If you have any questions or issues please send us a message on [Slack](https://nfcore.slack.com/channels/configs).