mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-31 11:42:12 -05:00
update README
This commit is contained in:
MaxUlysse
parent
028008c1d0
commit
209763620a
1 changed files with 60 additions and 32 deletions
92
README.md
92
README.md
|
|
@ -5,35 +5,40 @@
|
|||
A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
|
||||
|
||||
## Table of contents
|
||||
|
||||
* [Using an existing config](#using-an-existing-config)
|
||||
* [Configuration and parameters](#configuration-and-parameters)
|
||||
* [Offline usage](#offline-usage)
|
||||
* [Configuration and parameters](#configuration-and-parameters)
|
||||
* [Offline usage](#offline-usage)
|
||||
* [Adding a new config](#adding-a-new-config)
|
||||
* [Testing](#testing)
|
||||
* [Documentation](#documentation)
|
||||
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
|
||||
* [Testing](#testing)
|
||||
* [Documentation](#documentation)
|
||||
* [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 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)
|
||||
* [Pipeline Specific Documentation](#pipeline-specific-documentation)
|
||||
* [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)
|
||||
* [Help](#help)
|
||||
|
||||
## 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
|
||||
|
||||
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).
|
||||
|
||||
### 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`
|
||||
or `params.custom_config_base` set to the location of the directory containing the repository files:
|
||||
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` or `params.custom_config_base` set to the location of the directory containing the repository files:
|
||||
|
||||
```bash
|
||||
## 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/
|
||||
```
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
```bash
|
||||
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
|
||||
> files + singularity containers + institutional configs in one go for you, to make this process easier.
|
||||
> 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.
|
||||
|
||||
## 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
|
||||
|
||||
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.
|
||||
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.
|
||||
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.
|
||||
|
||||
### Testing
|
||||
|
||||
|
|
@ -80,7 +85,8 @@ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[pat
|
|||
|
||||
### 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.
|
||||
|
||||
|
|
@ -113,21 +119,35 @@ Currently documentation is available for the following systems:
|
|||
|
||||
### 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.
|
||||
|
||||
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.
|
||||
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.
|
||||
Here we will be adding an institutional pipeline-specific config.
|
||||
|
||||
: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
|
||||
|
||||
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
|
||||
* [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.**
|
||||
|
||||
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
|
||||
// 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
|
||||
|
||||
: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
|
||||
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
|
||||
|
||||
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).
|
||||
|
|
|
|||
Loading…
Reference in a new issue