Merge pull request #121 from MaxUlysse/Uppmax

Uppmax

README.md

@@ -4,9 +4,8 @@
 
 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)
@@ -14,11 +13,11 @@ A repository for hosting Nextflow configuration files containing custom paramete
   * [Checking user hostnames](#checking-user-hostnames)
   * [Testing](#testing)
   * [Documentation](#documentation)
-  * [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs)
+  * [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)
+  * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
 * [Help](#help)
 
 ## Using an existing config
@@ -164,10 +163,11 @@ Currently documentation is available for the following pipeline within the speci
 
 * ampliseq
   * [BINAC](docs/pipeline/ampliseq/binac.md)
-* sarek
-  * [MUNIN](docs/pipeline/sarek/munin.md)
 * eager
   * [SHH](docs/pipeline/eager/shh.md)
+* sarek
+  * [MUNIN](docs/pipeline/sarek/munin.md)
+  * [UPPMAX](docs/pipeline/sarek/uppmax.md)
 
 ### Enabling pipeline-specific configs within a pipeline
 

conf/pipeline/sarek/uppmax.config

@@ -0,0 +1,12 @@
+// 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'
+}
+
+params {
+  // Just useful until iGenomes is updated on UPPMAX
+  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" }
 }