Change to new conventions.

workflow/conf/biohpc.config

@@ -4,59 +4,59 @@ process {
   clusterOptions = '--hold'
 
   // Process specific configuration
-  $checkDesignFile {
+  withName: checkDesignFile {
     module = ['python/3.6.1-2-anaconda']
     executor = 'local'
   }
-  $trimReads {
+  withName: trimReads {
     module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
     cpus = 32
   }
-  $alignReads{
+  withName: alignReads{
     module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/1.6']
     cpus = 32
   }
-  $filterReads{
+  withName: filterReads{
     module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'sambamba/0.6.6', 'bedtools/2.26.0']
     cpus = 32
   }
-  $experimentQC {
+  withName: experimentQC {
     module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
     cpus = 32
   }
-  $convertReads {
+  withName: convertReads {
     module = ['python/3.6.1-2-anaconda',  'samtools/1.6', 'bedtools/2.26.0']
     cpus = 32
   }
-  $crossReads {
+  withName: crossReads {
     module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2']
     cpus = 32
   }
-  $defineExpDesignFiles {
+  withName: defineExpDesignFiles {
     module = ['python/3.6.1-2-anaconda']
     executor = 'local'
   }
-  $poolAndPsuedoReads {
+  withName: poolAndPsuedoReads {
     module = ['python/3.6.1-2-anaconda']
     executor = 'local'
   }
-  $callPeaksMACS {
+  withName: callPeaksMACS {
     module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0']
     cpus = 32
   }
-  $consensusPeaks {
+  withName: consensusPeaks {
     module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']
     executor = 'local'
   }
-  $peakAnnotation {
+  withName: peakAnnotation {
     module = ['R/3.4.1-gccmkl']
     executor = 'local'
   }
-  $diffPeaks {
+  withName: diffPeaks {
     module = ['R/3.4.1-gccmkl']
     cpus = 32
   }
-  $motifSearch {
+  withName: motifSearch {
     module = ['python/2.7.x-anaconda', 'meme/4.11.1-gcc-openmpi', 'bedtools/2.26.0']
     cpus = 32
   }