Merge pull request #160 from ewels/master

Merge czbiohub_aws_highpriority profile into czbiohub_aws

README.md

@@ -104,7 +104,6 @@ Currently documentation is available for the following systems:
 * [CFC](docs/cfc.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
-* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
 * [DENBI_QBIC](docs/denbi_qbic.md)
 * [EBC](docs/ebc.md)
 * [GENOTOUL](docs/genotoul.md)

bin/cchecker.py

@@ -45,11 +45,11 @@ def check_config(Config, Github):
             if re.search(regex, line):
                 hit = line.split('/')[2].split('.')[0]
                 config_profiles.add(hit.strip())
-    
-    ###Check Github Config now
+
+    ### Check Github Config now
     tests = set()
-    ###Ignore these profiles
-    ignore_me = ['czbiohub_aws_highpriority', 'czbiohub_aws']
+    ### Ignore these profiles
+    ignore_me = ['czbiohub_aws']
     tests.update(ignore_me)
     with open(Github, 'r') as ghfile:
         for line in ghfile:
@@ -58,11 +58,11 @@ def check_config(Config, Github):
                 profiles = line.split(':')[1].split(',')
                 for p in profiles:
                     tests.add(p.strip())
-   
+
     ###Check if sets are equal
     if tests == config_profiles:
         sys.exit(0)
-    else: 
+    else:
         #Maybe report what is missing here too
         print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
         print(config_profiles.symmetric_difference(tests))

conf/czbiohub_aws.config

@@ -135,3 +135,12 @@ params {
     }
   }
 }
+
+
+profiles {
+  highpriority {
+    process {
+      queue = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036'
+    }
+  }
+}

conf/czbiohub_aws_highpriority.config

@@ -1,12 +0,0 @@
-/*
- * -------------------------------------------------
- *  Nextflow config file for Chan Zuckerberg Biohub
- * -------------------------------------------------
- * Defines reference genomes, using iGenome paths
- * Imported under the default 'standard' Nextflow
- * profile in nextflow.config
- */
-
-process {
-  queue = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036'
-}

docs/czbiohub.md

@@ -122,3 +122,11 @@ For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annota
 
 >NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
 >NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+
+## High Priority Queue
+
+If you would like to run with the _High Priority_ queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
+
+To use it, submit your run with with `-profile czbiohub_aws,highpriority`.
+
+**Note that the order of config profiles here is important.** For example, `-profile highpriority,czbiohub_aws` will not work.

nfcore_custom.config

@@ -21,9 +21,6 @@ profiles {
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
-  czbiohub_aws_highpriority {
-                 includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
-                 includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
   ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }