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README.md
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@ -2,7 +2,7 @@
[![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg) [![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions.
## Table of contents ## Table of contents
@ -11,28 +11,36 @@ A repository for hosting nextflow config files containing custom parameters requ
* [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)
* [Checking user hostnames](#checking-user-hostnames) * [Checking user hostnames](#checking-user-hostnames)
* [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)
* [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [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
@ -45,28 +53,28 @@ 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
@ -74,12 +82,13 @@ If you want to add a new custom config file to `nf-core/configs` please test tha
```bash ```bash
## Example command for nf-core/rnaseq ## Example command for nf-core/rnaseq
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]' nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '/path/to/custom.config'
``` ```
### 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.
@ -113,7 +122,10 @@ 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`](https://github.com/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.
Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that. Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that.
@ -121,6 +133,87 @@ Commit and push these changes to your local clone on GitHub, and then [create a
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
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.
: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](https://github.com/nf-core/configs/blob/master/nfcore_custom.config), 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`](https://github.com/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.
### Pipeline-specific documentation
Currently documentation is available for the following pipeline within the specific profile:
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
### Enabling pipeline-specific configs within a pipeline
:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
[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 the following to `nextflow.config` **after** the code that loads the generic nf-core/configs config file:
```nextflow
// 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: ${params.custom_config_base}/pipeline/<PIPELINE>.config")
}
```
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/<PIPELINE>` GitHub repo with the appropriate information.
We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
### Create the pipeline-specific `nf-core/configs` files
:warning: This has to be done on a fork of the [`nf-core/configs`](https://github.com/nf-core/configs/) repository.
[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
And add or edit the following files in the local clone of your fork.
* `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
```Groovy
profiles {
<PROFILE> { includeConfig "${params.custom_config_base}/conf/pipeline/<PIPELINE>/<PROFILE>.config" }
}
```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<PIPELINE>.config` and 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>.md`
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.
* `README.md`
Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation
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.
In the pull-request description, add a link to the repository specific pull-request(s) that use this new code.
Both PRs will need to be merged at the approximately the same time.
## 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).

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@ -22,7 +22,7 @@ weblog{
params { params {
igenomes_base = '/nfsmounts/igenomes' igenomes_base = '/nfsmounts/igenomes'
max_memory = 60.GB max_memory = 498.GB
max_cpus = 20 max_cpus = 20
max_time = 140.h max_time = 140.h
} }

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@ -53,7 +53,7 @@ params {
// AWS configurations // AWS configurations
awsregion = "us-west-2" awsregion = "us-west-2"
awsqueue = "nextflow" awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'
igenomes_ignore = true igenomes_ignore = true
igenomesIgnore = true //deprecated igenomesIgnore = true //deprecated

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@ -11,7 +11,7 @@ singularity {
process { process {
executor = 'pbs' executor = 'pbs'
queue = 'batch' queue = { task.memory > 64.GB ? 'highmem': 'batch'}
} }
params { params {

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@ -1,8 +1,18 @@
//Profile config names for nf-core/configs // Profile config names for nf-core/configs
params { params {
// Specific nf-core/configs params
config_profile_contact = 'Szilveszter Juhos (@szilvajuhos)'
config_profile_description = 'MUNIN profile provided by nf-core/configs.' config_profile_description = 'MUNIN profile provided by nf-core/configs.'
config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_url = 'https://ki.se/forskning/barntumorbanken'
config_profile_url = ''
// Local AWS iGenomes reference file paths on munin
igenomes_base = '/data1/references/igenomes/'
// General cpus/memory/time requirements
max_cpus = 46
max_memory = 752.GB
max_time = 72.h
} }
process { process {
@ -10,9 +20,9 @@ process {
maxForks = 46 maxForks = 46
} }
// To use singularity, use nextflow run -profile munin,singularity
singularity { singularity {
enabled = true enabled = true
cacheDir = '/data1/containers/'
} }
// To use docker, use nextflow run -profile munin,docker // To use docker, use nextflow run -profile munin,docker
@ -21,13 +31,3 @@ docker {
mountFlags = 'z' mountFlags = 'z'
fixOwnership = true fixOwnership = true
} }
params {
// general params
max_memory = 752.GB
max_cpus = 46
max_time = 72.h
// Local AWS iGenomes reference file paths on munin
igenomes_base = '/data1/references/igenomes/'
}

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@ -0,0 +1,24 @@
// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
// Specific nf-core/sarek params
annotation_cache = true
pon = '/data1/PON/vcfs/BTB.PON.vcf.gz'
pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
snpEff_cache = '/data1/cache/snpEff/'
vep_cache = '/data1/cache/VEP/'
}
// Specific nf-core/sarek process configuration
process {
withLabel:sentieon {
if (params.sentieon) {
module = 'sentieon/201808.05'
container = null
}
}
}

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@ -0,0 +1,22 @@
# nf-core/configs: MUNIN sarek specific configuration
Extra specific configuration for sarek pipeline
## Usage
To use, run the pipeline with `-profile munin`.
This will download and launch the sarek specific [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
Example: `nextflow run nf-core/sarek -profile munin`
## Sarek specific configurations for MUNIN
Specific configurations for MUNIN has been made for sarek.
* Params `annotation_cache` set to `true`
* Path to `snpEff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Load module `Sentieon` for Processes with `sentieon` labels

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@ -0,0 +1,13 @@
/*
* -------------------------------------------------
* nfcore/sarek custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/sarek folder and imported
* under a profile name here.
*/
profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
}