Merge pull request #109 from apeltzer/master

TZ env for binac

README.md

@@ -1,4 +1,4 @@
-# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs)
+# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) <!-- omit in toc -->
 
 [![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
 
@@ -14,11 +14,11 @@ 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
@@ -154,6 +154,8 @@ 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/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" }
+}