Add in tss analysis.

workflow/conf/biohpc.config

@@ -61,16 +61,19 @@ params {
       bwa = '/project/shared/bicf_workflow_ref/GRCh38'
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
+      tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
     }
     'GRCh37' {
       bwa = '/project/shared/bicf_workflow_ref/GRCh37'
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
+      tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
     }
     'GRCm38' {
       bwa = '/project/shared/bicf_workflow_ref/GRCm38'
       genomesize = 'mm'
       chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
+      tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
     }
   }
 }

workflow/main.nf

@@ -12,6 +12,7 @@ params.genomes = []
 params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
+params.tssFile = params.genome ? params.genomes[ params.genome ].tssfile ?: false : false
 
 // Check inputs
 if( params.bwaIndex ){
@@ -35,6 +36,7 @@ designFile = params.designFile
 genomeSize = params.genomeSize
 chromSizes = params.chromSizes
 cutoffRatio = params.cutoffRatio
+tssFile = params.tssFile
 
 process checkDesignFile {