Resolve "Add mapping and trimming"

Closes #3 (closed)

workflow/conf/biohpc.config

+process {
+  executor = 'slurm'
+  queue='super'
+
+  // Process specific configuration
+  $checkDesignFile {
+    module = ['python/3.6.1-2-anaconda']
+    executor = 'local'
+  }
+  $trim_galore {
+    module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
+    cpus = 32
+  }
+  $alignReads{
+    module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/intel/1.3']
+    cpus = 32
+  }
+}
+
+params {
+  // Reference file paths on BioHPC
+  genomes {
+    'GRCh38' { bwa = '/project/shared/bicf_workflow_ref/GRCh38' }
+    'GRCh37' { bwa = '/project/shared/bicf_workflow_ref/GRCh37' }
+    'GRCm38' { bwa = '/project/shared/bicf_workflow_ref/GRCm38' }
+  }
+}
+
+trace {
+    enabled = true
+    file = 'pipeline_trace.txt'
+    fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}