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

@@ -78,7 +78,7 @@ params {
       genomesize = 'hs'
       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'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
     }
     'GRCh37' {
@@ -86,7 +86,7 @@ params {
       genomesize = 'hs'
       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'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt'
     }
     'GRCm38' {
@@ -94,7 +94,7 @@ params {
       genomesize = 'mm'
       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'
+      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
     }
   }