Merge pull request #8 from nf-core/master

Syncing

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
@@ -154,8 +154,12 @@ 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)
 
 ### Enabling pipeline-specific configs within a pipeline
 

conf/awsbatch.config

@@ -1,14 +1,16 @@
-//Nextflow config file for running on AWS batch
-
-params {
-  awsqueue = false
-  awsregion = 'eu-west-1'
-  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
-  config_profile_description = 'AWSBATCH Cloud Profile'
-  config_profile_name = 'AWSBATCH'
-  config_profile_url = 'https://aws.amazon.com/batch/'
-  tracedir = './'
-}
-
-process.executor = 'awsbatch'
-executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+//Nextflow config file for running on AWS batch
+params {
+  config_profile_description = 'AWSBATCH Cloud Profile'
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_url = 'https://aws.amazon.com/batch/'
+
+  awsqueue = false
+  awsregion = 'eu-west-1'
+  awscli = '/home/ec2-user/miniconda/bin/aws'
+  tracedir = './'
+}
+
+process.executor = 'awsbatch'
+process.queue = params.awsqueue
+aws.region = params.awsregion
+executor.awscli = params.awscli

conf/binac.config

@@ -7,6 +7,7 @@ params {
 
 singularity {
   enabled = true
+  envWhitelist = 'TZ'
 }
 
 process {

conf/crick.config

@@ -20,5 +20,5 @@ params {
   max_cpus = 32
   max_time = 72.h
 
-  igenomes_base = '/camp/svc/reference/Genomics/iGenomes'
+  igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes'
 }

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'
+}

conf/pipeline/sarek/munin.config

@@ -16,9 +16,7 @@ params {
 // Specific nf-core/sarek process configuration
 process {
   withLabel:sentieon {
-    if (params.sentieon) {
-      module = 'sentieon/201808.05'
-      container = null
-    }
+    module = {params.sentieon ? 'sentieon/201808.05' : null}
+    container = {params.sentieon ? null : container}
   }
 }

docs/awsbatch.md

@@ -1,4 +1,4 @@
 # nf-core/configs: awsbatch Configuration
 
 To be used with `awsbatch`.
-Custom queue and region can be entered with `params.awsqueue` and `params.region` respectively.
+Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.

docs/crick.md

@@ -9,13 +9,13 @@ Before running the pipeline you will need to load Nextflow and Singularity using
 ```bash
 ## Load Nextflow and Singularity environment modules
 module purge
-module load Nextflow/0.32.0
+module load Nextflow/19.10.0
 module load Singularity/2.6.0-foss-2016b
 ```
 
-A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
+A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
 
-Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions).
+Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions).
 
 All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
 

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" }
+}