1.2.4

buildContainers.nf

@@ -36,7 +36,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.3'
+version = '1.2.4'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented

buildReferences.nf

@@ -39,7 +39,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.3'
+version = '1.2.4'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented

configuration/uppmax-localhost.config

@@ -129,6 +129,14 @@ process {
   }
   $RunSamtoolsStats {
   }
+  $RunSingleManta {
+    cpus = 16
+    memory = {params.totalMemory}
+  }
+  $RunSingleStrelka {
+    cpus = 16
+    memory = {params.totalMemory}
+  }
   $RunSnpeff {
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
     memory = {params.totalMemory} // TODO Does SnpEff really require that much?

configuration/uppmax-slurm.config

@@ -132,6 +132,11 @@ process {
     cpus = 1
     time = {params.runTime * task.attempt}
   }
+  $RunSingleManta {
+  }
+  $RunSingleStrelka {
+    time = {params.runTime * task.attempt}
+  }
   $RunSnpeff {
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }

main.nf

@@ -62,7 +62,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.3'
+version = '1.2.4'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented

nextflow.config

@@ -15,7 +15,6 @@ params { // default value for params
   genome = 'GRCh38'
   help = false
   project = ''
-  vcflist =''
   verbose = false
   version = false
 }