Resolve "annotate peaks"

Closes #47 (closed) Change Annotate peaks step to call reference from gencode gtf files instead of TxDb and org libraries.

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• This comment contains a description of changes (with reason)
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• CHANGELOG.md is updated

workflow/conf/biohpc.config

@@ -74,25 +74,28 @@ params {
   // Reference file paths on BioHPC
   genomes {
     'GRCh38' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCh38'
+      bwa = '/project/shared/bicf_workflow_ref/human/GRCh38'
       genomesize = 'hs'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/GRCh38/gencode.gtf'
+      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh38/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/human/GRCh38/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
     }
     'GRCh37' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCh37'
+      bwa = '/project/shared/bicf_workflow_ref/human/GRCh37'
       genomesize = 'hs'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/GRCh37/gencode.gtf'
+      chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh37/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/human/GRCh37/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt'
     }
     'GRCm38' {
-      bwa = '/project/shared/bicf_workflow_ref/GRCm38'
+      bwa = '/project/shared/bicf_workflow_ref/mouse/GRCm38'
       genomesize = 'mm'
-      chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
-      fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/GRCm38/gencode.gtf'
+      chromsizes = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genomefile.txt'
+      fasta = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genome.fa'
+      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.gtf'
+      geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
     }
   }
 }