Merge pull request #11 from nf-core/master

Get latest changes

conf/bi.config

@@ -4,17 +4,11 @@ params{
   config_profile_url = 'https://www.boehringer-ingelheim.com/'
 }
 
-params.globalConfig = set_global_config()
+params.globalConfig = System.getenv('NXF_GLOBAL_CONFIG')
-
+if(params.globalConfig == null)
-
+{
-def set_global_config() {
+    def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile."
-  def config = System.getenv('NXF_GLOBAL_CONFIG')
+    System.err.println(errorMessage)
-  if(config  == null)
+}else{
-  {
+    includeConfig params.globalConfig
-      def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile."
-      System.err.println(errorMessage)
-  }else{
-    includeConfig config
-  }
-  return config
 }

conf/crick.config

@@ -11,7 +11,6 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load Singularity/2.6.0-foss-2016b'
   executor = 'slurm'
 }
 

conf/pipeline/eager/shh.config

@@ -76,7 +76,6 @@ profiles {
       bwaalnn = 0.01
       bwaalnl = 16
       run_bam_filtering = true
-      bam_discard_unmapped = true
       bam_unmapped_type = 'fastq'
       run_metagenomic_screening = true
       metagenomic_tool = 'malt'

conf/shh.config

@@ -33,6 +33,10 @@ profiles {
     params {
       config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
     }
+    // delete when CDAG will be fixed
+    process {
+      queue = 'long'
+    }
   }
   sdag {
     params {

docs/crick.md

@@ -10,7 +10,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using
 ## Load Nextflow and Singularity environment modules
 module purge
 module load Nextflow/19.10.0
-module load Singularity/2.6.0-foss-2016b
+module load Singularity
 ```
 
 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).