Make MultiQC run locally on uppmax for an internet connection.

Gregor-Mendel-Institute · Jun 12, 2017 · c49bf61 · c49bf61
1 parent 12a3889
commit c49bf61
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 8 deletions.
diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config
@@ -10,6 +10,10 @@ vim: syntax=groovy
  * for this queue.
  */
 
+executor {
+  name = 'slurm'
+  queueSize = 1
+}
 
 process {
   executor = 'slurm'
@@ -18,11 +22,11 @@ process {
   memory = { 8.GB * task.attempt }
   time = 1.h
   clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
-  
+
   errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' }
   maxRetries = 3
   maxErrors = '-1'
-  
+
   // Environment modules and resource requirements
   $fastqc {
     module = ['bioinfo-tools', 'FastQC']
@@ -62,14 +66,15 @@ process {
     memory = { 32.GB * task.attempt }
     errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
   }
-  // NB: Overwrite this in your user config file (~/.nextflow/config)
+  // NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
   // if you have your own installation of MultiQC outside of the environment module system.
-  // eg: Add the line: params.$multiqc.module = ''
+  // eg: Add the line: process.$multiqc.module = []
   $multiqc {
     module = ['bioinfo-tools', 'MultiQC']
+    executor = 'local'
     errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
   }
-  
+
   $makeBwaMemIndex {
     module = ['bioinfo-tools', 'bwa', 'bwa-meth', 'samtools/1.3']
   }
@@ -103,7 +108,6 @@ process {
     memory = { 48.GB * task.attempt }
   }
 
-
 }
 
 params {
@@ -201,3 +205,14 @@ params {
     }
   }
 }
+
+
+timeline {
+  enabled = true
+  file = "${params.outdir}/NGI-MethylSeq_timeline.html"
+}
+trace {
+  enabled = true
+  file = "${params.outdir}/NGI-MethylSeq_trace.txt"
+}
+
diff --git a/conf/uppmax.config b/conf/uppmax.config
@@ -65,11 +65,12 @@ process {
     time = { 6.h * task.attempt }
     errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
   }
-  // NB: Overwrite this in your user config file (~/.nextflow/config)
+  // NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
   // if you have your own installation of MultiQC outside of the environment module system.
-  // eg: Add the line: params.$multiqc.module = ''
+  // eg: Add the line: process.$multiqc.module = []
   $multiqc {
     module = ['bioinfo-tools', 'MultiQC']
+    executor = 'local'
     errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
   }