add UPPMAX specific sarek config

README.md

@@ -4,22 +4,21 @@
 
 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
 

conf/pipeline/sarek/uppmax.config

@@ -0,0 +1,17 @@
+// 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'
+}

docs/pipeline/sarek/uppmax.md

@@ -0,0 +1,18 @@
+# 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`

pipeline/sarek.config

@@ -10,4 +10,5 @@
 
 profiles {
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
+  uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
 }