Resolve "Astrocyte fixes"

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• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
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Closes #40 (closed)

workflow/main.nf

@@ -52,29 +52,10 @@ if (params.astrocyte) {
   params.geneNames = params.genome ? params.genomes[ params.genome ].geneNames ?: false : false
 }
 
-
-
-
-genomes {
-  'GRCh38' {
-
-    blacklistfile = '/project/shared/bicf_workflow_ref/GRCh38/ENCFF356LFX.bed'
-    geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
-  }
-  'GRCm38' {
-    bwa = '/project/shared/bicf_workflow_ref/GRCm38'
-    genomesize = 'mm'
-    chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
-    gtffile = '/project/shared/bicf_workflow_ref/GRCm38/gencode.vM20.annotation.gtf'
-    blacklistfile = '/project/shared/bicf_workflow_ref/GRCm38/ENCFF999QPV.bed'
-    geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
-  }
-}
-
 // Check inputs
 if(params.bwa) {
   bwa= Channel
-    .fromPath(params.bwa\)
+    .fromPath(params.bwa)
     .ifEmpty { exit 1, "BWA index not found: ${params.bwaIndex}" }
 } else {
   exit 1, "No reference genome specified."