Adjust custom pipeline config for ampliseq on BINAC

README.md

@@ -6,20 +6,21 @@ A repository for hosting Nextflow configuration files containing custom paramete
 
 ## Table of contents
 
-* [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)
+* [<img src="docs/images/nfcore-configs_logo.png" alt="nf-core/configs" title="nf-core/configs">](#img-srcdocsimagesnfcore-configs_logopng-altnf-coreconfigs-titlenf-coreconfigs)
+  * [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
 
@@ -154,6 +155,8 @@ 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

conf/binac.config

@@ -10,10 +10,6 @@ singularity {
   envWhitelist = 'TZ'
 }
 
-env {
-     TZ='Europe/Berlin'
-}
-
 process {
   beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'pbs'

conf/pipeline/ampliseq/binac.config

@@ -0,0 +1,11 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_description = 'nf-core/ampliseq BINAC profile provided by nf-core/configs'
+}
+
+env {
+     TZ='Europe/Berlin'
+}

docs/pipeline/ampliseq/binac.md

@@ -0,0 +1,17 @@
+# nf-core/configs: binac ampliseq specific configuration
+
+Extra specific configuration for the ampliseq pipeline.
+
+## Usage
+
+To use, run the pipeline with `-profile binac`.
+
+This will download and launch the ampliseq specific [`binac.config`](../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
+
+Example: `nextflow run nf-core/ampliseq -profile binac`
+
+## ampliseq specific configurations for binac
+
+Specific configurations for BINAC has been made for ampliseq.
+
+* Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue

pipeline/ampliseq.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/ampliseq custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/ampliseq folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
+}