Structured config file

Author: viklund

nextflow.config

@@ -1,9 +1,12 @@
 params {
-    steps = 'manta,vep' // Change on commandline --steps x,y,z
+    // Command line parameters
+    bam = "" // The bamfile, preferrably supply on commandline ( --bam )
     project = "" // Set project or supply on commandline ( --project )
+    steps = 'manta,vep' // Change on commandline --steps x,y,z
     outdir = "results"
     prefix = ''
 
+    // Reference assemblies
     ref_fasta = "/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37/human_g1k_v37.fasta"
     assembly = 'GRCh37'
 
@@ -20,6 +23,7 @@ params {
         vt = "vt/0.5772"
     }
 
+    // Runtimes for different parts of the workflow
     runtime {
         simple = '30m'    // Short simple shell jobs
         fermikit = '24h' // Fermikit is the longest running of them all