change FullPathToFq to Fq in design file

README.md

 ## Variant Analysis Worklow
 
+```
 module load nextflow/0.24.1-SNAPSHOT
 nextflow run workflow/main.nf
+```
\ No newline at end of file

docs/index.md

@@ -63,9 +63,9 @@ The following columns are necessary, must be named as in template and can be in
 	2= Case or Diseaes Phenotype, 1= Healthy Control
     Gender
 	1=male, 2=female
-    FullPathToFqR1
+    FqR1
 	Name of the fastq file R1
-    FullPathToFqR2
+    FqR2
 	Name of the fastq file R2
 
 There are some optional columns that might help with the analysis:

workflow/main.nf

@@ -42,8 +42,8 @@ new File(params.design).withReader { reader ->
     def hline = reader.readLine()
     def header = hline.split("\t")
     prefixidx = header.findIndexOf{it == 'SampleID'};
-    oneidx = header.findIndexOf{it == 'FullPathToFqR1'};
-    twoidx = header.findIndexOf{it == 'FullPathToFqR2'};
+    oneidx = header.findIndexOf{it == 'FqR1'};
+    twoidx = header.findIndexOf{it == 'FqR2'};
     if (twoidx == -1) {
        twoidx = oneidx
        }