Whitespace cleanup

Author: viklund

config/devcore.config

@@ -1,12 +1,11 @@
 process {
+    clusterOptions = {
+        "-A $params.project"
+    }
 
-   clusterOptions = {
-       "-A $params.project"
-   }
-   errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }
-   queue = 'devcore'
-   executor = 'slurm'
-
-   time = '1h'
+    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }
+    queue = 'devcore'
+    executor = 'slurm'
 
+    time = '1h'
 }

config/milou.config

@@ -1,47 +1,46 @@
 process {
+    $index_bamfile {
+        module = ['bioinfo-tools', 'samtools/1.3']
+    }
 
-  $index_bamfile {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-
-  $manta {
-    maxRetries = 3
-    cpus = 16
-    module = ['bioinfo-tools', 'manta/1.0.3']
-  }
+    $manta {
+        maxRetries = 3
+        cpus = 16
+        module = ['bioinfo-tools', 'manta/1.0.3']
+    }
 
-  $create_fastq {
-    module = ['bioinfo-tools', 'samtools/1.3']
+    $create_fastq {
+        module = ['bioinfo-tools', 'samtools/1.3']
     }
 
-  $fermikit {
-    maxRetries = 3
-    cpus = 16
-    module = ['bioinfo-tools', 'samtools/1.3', 'fermikit/r178', "vcftools/0.1.14", "tabix/0.2.6"]
+    $fermikit {
+        maxRetries = 3
+        cpus = 16
+        module = ['bioinfo-tools', 'samtools/1.3', 'fermikit/r178', "vcftools/0.1.14", "tabix/0.2.6"]
     }
 
-  $artifact_mask_vcfs {
-    module = ['bioinfo-tools', 'BEDTools/2.25.0']
+    $artifact_mask_vcfs {
+        module = ['bioinfo-tools', 'BEDTools/2.25.0']
     }
 
-  $swegen_mask_vcfs {
-    module = ['bioinfo-tools', 'BEDTools/2.25.0']
+    $swegen_mask_vcfs {
+        module = ['bioinfo-tools', 'BEDTools/2.25.0']
     }
 
-  $intersect_files {
-    module = ['bioinfo-tools', 'BEDTools/2.25.0']
+    $intersect_files {
+        module = ['bioinfo-tools', 'BEDTools/2.25.0']
     }
 
-  $normalize_vcf {
-    module = ['bioinfo-tools', 'vt/0.5772']
+    $normalize_vcf {
+        module = ['bioinfo-tools', 'vt/0.5772']
     }
 
-  $variant_effect_predictor {
-    cpus = 4
-    module = ['bioinfo-tools', 'vep/84']
+    $variant_effect_predictor {
+        cpus = 4
+        module = ['bioinfo-tools', 'vep/84']
     }
 
-  $snpEff {
-    module = ['bioinfo-tools', 'snpEff/4.2', 'vt/0.5772']
+    $snpEff {
+        module = ['bioinfo-tools', 'snpEff/4.2', 'vt/0.5772']
     }
 }

config/standard.config

@@ -1,5 +1,4 @@
 process {
-
     clusterOptions = {
         "-A $params.project"
     }

main.nf

@@ -246,7 +246,7 @@ process intersect_files {
         fermi_vcf=${vcfs[1]}
         manta_vcf=${vcfs[0]}
     fi
-    
+
     OUTNAME=`basename \$fermi_vcf|sed 's/fermikit_//;s/.vcf//'`
     ## Create intersected vcf files
     for WORD in DEL INS DUP; do

nextflow.config

@@ -57,5 +57,3 @@ executor {
         queueSize = 1
     }
 }
-
-