A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different institutions.
The Nextflow -c 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.
This is where nf-core/configs comes in.
No need to write a custom config, simply run nextflow run <nf-core pipeline> -profile <hpc_name> and everything is configured for you!
All currently supported HPCs and infrastructure can be seen on the nf-core website.
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 on your HPC you can add and customize the Nextflow singularity scope in your config file.
Similarly, you can define a Nextflow executor 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.
To use nf-core pipelines offline, we recommend using the nf-core download helper tool. This will download both the pipeline files and also the config profiles from nf-core/configs. The pipeline files are then edited to load the configs from their relative file path correctly.
# Download the workflow + transfer to offline cluster
nf-core download rnaseq
scp nf-core-rnaseq-3.0.tar.gz me@myserver.com:/path/to/workflows # or however you prefer to transfer files to your offline cluster
# Connect to offline cluster
ssh me@myserver.com
# Extract workflow files
cd /path/to/workflows
tar -xzf nf-core-rnaseq-3.0.tar.gz
# Run workflow
cd /path/to/data
nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile myclusterIf required, you can instead download the nf-core/configs files yourself and customise the --custom_config_base / params.custom_config_base parameter in each pipeline to to set to the location of the configs directory.
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 for examples.
Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described above), and then continuing with the next steps.
Warning
In the near future, nf-core/configs will require adherence to Nextflow's 'strict' syntax. Ensure you read the documentation here and here on how to correctly write and format your config. Use of the language server through the VSCode Extension can be helpful for identifying syntax errors.
Note
In your config file, 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.
Note
If you try to specify a shell environment variable within your profile, in some cases you may get an error during testing of something like Unknown config attribute env.USER_SCRATCH -- check config file: /home/runner/work/configs/configs/nextflow.config (where the bash environment variable is $USER_SCRATCH).
This is because the GitHub runner used for CI testing will not have your institutional environment variables set. To fix this you can define this as an internal variable, and set a fallback value for that variable. A good example is in the VSC_UGENT profile.
If you want to add a new custom config file to nf-core/configs please test that your pipeline of choice runs as expected by using the -c parameter.
## Example command for nf-core/rnaseq
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '/path/to/custom.config'You will have to create a Markdown document outlining the details required to use the custom config file within your organisation. You might orientate yourself using the Template that we provide and filling out the information for your cluster there.
See nf-core/configs/docs for examples.
Warning
Before you start, make sure you are a part of the nf-core GitHub organisation! More information on joining can be found here.
Fork 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/directory -
add the documentation file to the
docs/directory -
edit and add your custom profile to the
nfcore_custom.configfile in the top-level directory of the clone -
add your profile name to GitHub Actions YAML
profile:scope (under strategy matrix) in.github/workflows/main.yml.-
If you forget to do this the tests will fail with the error in GitHub Actions:
```bash Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML. set(['<profile_name>']) ##[error]Process completed with exit code 1. ```
-
Warning
In the near future, nf-core/configs will require adherence to Nextflow's 'strict' syntax. Ensure you read the documentation here and here on how to correctly write and format your config. Use of the language server through the VSCode Extension can be helpful for identifying syntax errors.
Once all the files have been added and updated, commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/configs GitHub repo with the appropriate information.
Please request review from @nf-core/maintainers and/or on #request-review on the nf-core slack, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
Note
Once you get approval, you as the pull request author MUST merge the pull request. Community members cannot be held responsible for the use config on your infrastructure as they do not have permission to test on your infrastructure, therefore the PR author should be the person to merge in the config. If you do not see the 'merge' button at the bottom of the PR, ensure you're in nf-core GitHub organisation! More information on joining can be found here.
Warning
Before you start, make sure you are a part of the nf-core GitHub organisation! More information on joining can be found here.
Sometimes it may be desirable to have configuration options for an institute that are specific to a single nf-core pipeline. Such options should not be added to the main institutional config, as this will be applied to all pipelines. Instead, we can create a pipeline-specific institutional config file.
Existing pipeline-specific HPC and infrastructure configs can be seen on the nf-core website under the 'pipeline configs column.
The following steps are similar to the instructions for standard institutional config, however using
pipelinevariants of folders e.g.,conf/pipeline/or underpipeline/
Warning
Remember to replace the <PIPELINE> and <PROFILE> placeholders with the pipeline name and profile name in the following examples
Institutional configs work because the pipeline nextflow.config file loads the nf-core/configs/nfcore_custom.config config file, which in turn loads the institutional configuration file based on the profile <PROFILE> supplied on the command line.
To add in pipeline-specific institutional configs, we add a second includeConfig call in the pipeline nextflow.config file, which loads the pipeline/<PIPELINE>.config file from the nf-core/configs repo.
This file has <PIPELINE> specific institution configuration again with different profiles <PROFILE>.
The pipeline nextflow.config file should first load the generic institutional configuration file and then the pipeline-specific institutional configuration file.
Each configuration file will add new params and overwrite the params already existing.
Note that pipeline-specific configs are not required and should only be added if needed.
[!WARNING] > This has to be done on a fork of the
nf-core/<PIPELINE>repository.
Fork the nf-core/<PIPELINE> repository to your own GitHub account.
Within the local clone of your fork, if not already present, add the following to nextflow.config after the code that loads the generic nf-core/configs config file:
// Load nf-core/<PIPELINE> custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/pipeline/<PIPELINE>.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/<PIPELINE> profiles: ${params.custom_config_base}/pipeline/<PIPELINE>.config")
}Commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/<PIPELINE> GitHub repo with the appropriate information.
We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
Warning
This has to be done on a fork of the nf-core/configs repository.
Fork the nf-core/configs repository to your own GitHub account.
And add or edit the following files in the local clone of your fork:
-
pipeline/<PIPELINE>.configIf not already created, create the
pipeline/<PIPELINE>.configfile, and add your custom profile to the profile scopeprofiles { <PROFILE> { includeConfig "${params.custom_config_base}/conf/pipeline/<PIPELINE>/<PROFILE>.config" } } -
conf/pipeline/<PIPELINE>/<PROFILE>.configAdd the custom configuration file to the
conf/pipeline/<PIPELINE>/directory. Make sure to add an extraparamssection withparams.config_profile_description,params.config_profile_contactto the top ofpipeline/<PIPELINE>.configand 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. -
docs/pipeline/<PIPELINE>/<PROFILE>.mdAdd the documentation file to the
docs/pipeline/<PIPELINE>/directory. You will also need to edit and add your custom profile to theREADME.mdfile in the top-level directory of the clone.
Warning
In the near future, nf-core/configs will require adherence to Nextflow's 'strict' syntax. Ensure you read the documentation here and here on how to correctly write and format your config. Use of the language server through the VSCode Extension can be helpful for identifying syntax errors.
Commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/configs GitHub repo with the appropriate information.
In the pull-request description, add a link to the repository specific pull-request(s) that use this new code.
Please request review from @nf-core/maintainers and/or on #request-review on the nf-core slack, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible. Both PRs will need to be merged at the approximately the same time.
Note
Once you get approval, you as the pull request author MUST merge the pull request. Community members cannot be held responsible for the use config on your infrastructure as they do not have permission to test on your infrastructure, therefore the PR author should be the person to merge in the config. If you do not see the 'merge' button at the bottom of the PR, ensure you're in nf-core GitHub organisation! More information on joining can be found here.
If you have any questions or issues please send us a message on Slack.