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Merge branch 'sarek' of github.com:MaxUlysse/nf-core_configs into sarek

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MaxUlysse 2019-11-26 15:22:02 +01:00
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README.md
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@ -130,19 +130,22 @@ We will be notified automatically when you have created your pull request, and p
## Adding a new pipeline-specific config ## Adding a new pipeline-specific config
Here we will be adding an institutional 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: Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines. :warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` placeholders with the pipeline name and profile name in the following examples
: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>`. 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.
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>`. 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>`.
`nextflow.config` from pipeline will load first institutional configuration file and then the pipeline-specific institutional configuration file. 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. 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. Note that pipeline-specific configs are not required and should only be added if needed.
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. 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
@ -157,9 +160,9 @@ Currently documentation is available for the following pipeline within the speci
: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.**
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` repository to your own GitHub account. [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` 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:
```Groovy ```nextflow
// Load nf-core/<PIPELINE> custom profiles from different Institutions // Load nf-core/<PIPELINE> custom profiles from different Institutions
try { try {
includeConfig "${params.custom_config_base}/pipeline/<PIPELINE>.config" includeConfig "${params.custom_config_base}/pipeline/<PIPELINE>.config"
@ -190,6 +193,7 @@ 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. 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.
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

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conf/munin.config
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@ -20,7 +20,6 @@ process {
maxForks = 46 maxForks = 46
} }
// To use singularity, use nextflow run -profile munin
singularity { singularity {
enabled = true enabled = true
cacheDir = '/data1/containers/' cacheDir = '/data1/containers/'