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Merge pull request #85 from MaxUlysse/sarek
Adding a pipeline specific config for a specific system
This commit is contained in:
Maxime Garcia
GitHub
commit
64ff62de2c
5 changed files with 185 additions and 33 deletions
131
README.md
131
README.md
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@ -2,7 +2,7 @@
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[](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
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A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
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A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions.
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## Table of contents
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@ -11,28 +11,36 @@ A repository for hosting nextflow config files containing custom parameters requ
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Adding a new config](#adding-a-new-config)
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* [Checking user hostnames](#checking-user-hostnames)
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* [Checking user hostnames](#checking-user-hostnames)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Help](#help)
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## Using an existing config
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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.
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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.
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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.
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### Configuration and parameters
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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.
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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.
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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.
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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.
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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.
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In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
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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).
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### Offline usage
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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`
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or `params.custom_config_base` set to the location of the directory containing the repository files:
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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.
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Then run the pipeline with `--custom_config_base` or `params.custom_config_base` set to the location of the directory containing the repository files:
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```bash
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## Download and unzip the config files
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@ -45,28 +53,28 @@ cd /path/to/my/data
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nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
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```
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Alternatively, instead of using the configuration profiles from this repository, you can run your
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pipeline directly calling the single institutional config file that you need with the `-c` parameter.
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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.
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```bash
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nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
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```
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> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
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> files + singularity containers + institutional configs in one go for you, to make this process easier.
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> 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.
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## Adding a new config
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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.
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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.
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You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
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See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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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.
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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.
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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.
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## Checking user hostnames
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### Checking user hostnames
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If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile.
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Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name.
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If the user's hostname contains this string at the start of a run or when a run fails and their profile
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does not contain the profile name, a warning message will be printed.
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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.
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### Testing
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@ -74,12 +82,13 @@ If you want to add a new custom config file to `nf-core/configs` please test tha
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```bash
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## Example command for nf-core/rnaseq
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nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'
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nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '/path/to/custom.config'
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```
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### Documentation
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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.
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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.
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You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there.
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See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.
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@ -113,7 +122,10 @@ Currently documentation is available for the following systems:
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### Uploading to `nf-core/configs`
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[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.
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[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.
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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.
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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.
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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.
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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.
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@ -121,6 +133,87 @@ Commit and push these changes to your local clone on GitHub, and then [create a
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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.
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## Adding a new pipeline-specific config
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Sometimes it may be desirable to have configuration options for an institute that are specific to a single nf-core pipeline.
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Such options should not be added to the main institutional config, as this will be applied to all pipelines.
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Instead, we can create a pipeline-specific institutional config file.
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:warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` placeholders with the pipeline name and profile name in the following examples
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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.
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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.
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This file has `<PIPELINE>` specific institution configuration again with different profiles `<PROFILE>`.
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The pipeline `nextflow.config` file should first load the generic institutional configuration file and then the pipeline-specific institutional configuration file.
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Each configuration file will add new params and overwrite the params already existing.
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Note that pipeline-specific configs are not required and should only be added if needed.
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### Pipeline-specific documentation
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Currently documentation is available for the following pipeline within the specific profile:
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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### Enabling pipeline-specific configs within a pipeline
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:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
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[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` repository to your own GitHub account.
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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:
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```nextflow
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// Load nf-core/<PIPELINE> custom profiles from different Institutions
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try {
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includeConfig "${params.custom_config_base}/pipeline/<PIPELINE>.config"
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} catch (Exception e) {
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System.err.println("WARNING: Could not load nf-core/config/<PIPELINE> profiles: ${params.custom_config_base}/pipeline/<PIPELINE>.config")
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}
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```
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/<PIPELINE>` GitHub repo with the appropriate information.
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We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.
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### Create the pipeline-specific `nf-core/configs` files
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:warning: This has to be done on a fork of the [`nf-core/configs`](https://github.com/nf-core/configs/) repository.
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[Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account.
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And add or edit the following files in the local clone of your fork.
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* `pipeline/<PIPELINE>.config`
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If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
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```Groovy
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profiles {
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<PROFILE> { includeConfig "${params.custom_config_base}/conf/pipeline/<PIPELINE>/<PROFILE>.config" }
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}
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```
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* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
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Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
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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.
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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.
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* `docs/pipeline/<PIPELINE>/<PROFILE>.md`
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Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory.
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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.
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* `README.md`
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Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation
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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.
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In the pull-request description, add a link to the repository specific pull-request(s) that use this new code.
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Both PRs will need to be merged at the approximately the same time.
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## Help
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If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).
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If you have any questions or issues please send us a message on [Slack](https://nfcore.slack.com/channels/configs).
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//Profile config names for nf-core/configs
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// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Szilveszter Juhos (@szilvajuhos)'
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config_profile_description = 'MUNIN profile provided by nf-core/configs.'
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config_profile_contact = 'Szilveszter Juhos (@szilva)'
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config_profile_url = ''
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config_profile_url = 'https://ki.se/forskning/barntumorbanken'
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// Local AWS iGenomes reference file paths on munin
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igenomes_base = '/data1/references/igenomes/'
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// General cpus/memory/time requirements
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max_cpus = 46
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max_memory = 752.GB
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max_time = 72.h
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}
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process {
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maxForks = 46
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}
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// To use singularity, use nextflow run -profile munin,singularity
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singularity {
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enabled = true
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cacheDir = '/data1/containers/'
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}
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// To use docker, use nextflow run -profile munin,docker
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mountFlags = 'z'
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fixOwnership = true
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}
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params {
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// general params
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max_memory = 752.GB
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max_cpus = 46
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max_time = 72.h
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// Local AWS iGenomes reference file paths on munin
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igenomes_base = '/data1/references/igenomes/'
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}
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24
conf/pipeline/sarek/munin.config
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24
conf/pipeline/sarek/munin.config
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// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
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config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
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// Specific nf-core/sarek params
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annotation_cache = true
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pon = '/data1/PON/vcfs/BTB.PON.vcf.gz'
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pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
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snpEff_cache = '/data1/cache/snpEff/'
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vep_cache = '/data1/cache/VEP/'
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}
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// Specific nf-core/sarek process configuration
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process {
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withLabel:sentieon {
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if (params.sentieon) {
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module = 'sentieon/201808.05'
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container = null
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}
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}
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}
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22
docs/pipeline/sarek/munin.md
Normal file
22
docs/pipeline/sarek/munin.md
Normal file
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# nf-core/configs: MUNIN sarek specific configuration
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Extra specific configuration for sarek pipeline
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## Usage
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To use, run the pipeline with `-profile munin`.
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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.
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Example: `nextflow run nf-core/sarek -profile munin`
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## Sarek specific configurations for MUNIN
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Specific configurations for MUNIN has been made for sarek.
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* Params `annotation_cache` set to `true`
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* Path to `snpEff_cache`: `/data1/cache/snpEff/`
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* Path to `vep_cache`: `/data1/cache/VEP/`
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* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
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* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
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* Load module `Sentieon` for Processes with `sentieon` labels
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13
pipeline/sarek.config
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13
pipeline/sarek.config
Normal file
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/*
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* -------------------------------------------------
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* nfcore/sarek custom profile Nextflow config file
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* -------------------------------------------------
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* Config options for custom environments.
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* Cluster-specific config options should be saved
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* in the conf/pipeline/sarek folder and imported
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* under a profile name here.
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*/
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profiles {
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munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
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}
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