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add UPPMAX specific sarek config

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MaxUlysse 2020-02-20 17:14:18 +01:00
parent a5e183266e
commit aa905cd645
4 changed files with 85 additions and 49 deletions

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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 <!-- omit in toc -->
* [Table of contents](#table-of-contents)
* [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames)
* [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 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)
- [Using an existing config](#using-an-existing-config)
- [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage)
- [Adding a new config](#adding-a-new-config)
- [Checking user hostnames](#checking-user-hostnames)
- [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 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)
## Using an existing config
@ -94,30 +93,30 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems:
* [AWSBATCH](docs/awsbatch.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CBE](docs/cbe.md)
* [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md)
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md)
* [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md)
* [HEBBE](docs/hebbe.md)
* [KRAKEN](docs/kraken.md)
* [MUNIN](docs/munin.md)
* [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)
* [UPPMAX](docs/uppmax.md)
* [UZH](docs/uzh.md)
- [AWSBATCH](docs/awsbatch.md)
- [BIGPURPLE](docs/bigpurple.md)
- [BINAC](docs/binac.md)
- [CBE](docs/cbe.md)
- [CCGA](docs/ccga.md)
- [CCGA_DX](/docs/ccga_dx.md)
- [CFC](docs/binac.md)
- [CRICK](docs/crick.md)
- [CZBIOHUB_AWS](docs/czbiohub.md)
- [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
- [DENBI_QBIC](docs/denbi_qbic.md)
- [GENOTOUL](docs/genotoul.md)
- [GENOUEST](docs/genouest.md)
- [GIS](docs/gis.md)
- [HEBBE](docs/hebbe.md)
- [KRAKEN](docs/kraken.md)
- [MUNIN](docs/munin.md)
- [PASTEUR](docs/pasteur.md)
- [PHOENIX](docs/phoenix.md)
- [PRINCE](docs/prince.md)
- [SHH](docs/shh.md)
- [UCT_HEX](docs/uct_hex.md)
- [UPPMAX](docs/uppmax.md)
- [UZH](docs/uzh.md)
### Uploading to `nf-core/configs`
@ -154,12 +153,13 @@ Note that pipeline-specific configs are not required and should only be added if
Currently documentation is available for the following pipeline within the specific profile:
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
* eager
* [SHH](docs/pipeline/eager/shh.md)
- ampliseq
- [BINAC](docs/pipeline/ampliseq/binac.md)
- sarek
- [MUNIN](docs/pipeline/sarek/munin.md)
- [UPPMAX](docs/pipeline/sarek/uppmax.md)
- eager
- [SHH](docs/pipeline/eager/shh.md)
### Enabling pipeline-specific configs within a pipeline
@ -188,7 +188,7 @@ We will be notified automatically when you have created your pull request, and p
[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`
- `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
@ -198,18 +198,18 @@ profiles {
}
```
* `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`
- `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`
- `README.md`
Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation

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// sarek/uppmax specific profile config
params {
config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs'
}
if (hostname ==~ "i.*") {
singularity {
cacheDir = "${params.containers_path}"
}
}
params {
igenomeIgnore = true
genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle'
}

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# nf-core/configs: uppmax sarek specific configuration
Extra specific configuration for sarek pipeline
## Usage
To use, run the pipeline with `-profile uppmax`.
This will download and launch the sarek specific [`uppmax.config`](../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
Example: `nextflow run nf-core/sarek -profile uppmax`
## Sarek specific configurations for uppmax clusters
Specific configurations for uppmax clusters has been made for sarek.
* Set paths to reference genomes
* Set path to singularity containers for `irma`

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profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
}