move annotation files to location section of settings

BIMSBbioinfo · Jul 19, 2024 · e61e75d · e61e75d
1 parent 5a7823b
commit e61e75d
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in
@@ -2,6 +2,11 @@ locations:
   input-dir: /path/to/reads/
   output-dir: /path/to/output/
   genome-fasta: /path/to/genome.fasta
+  # UCSC annotation tables fetched from table browser in BED format.
+  # CpG island predictions
+  cpgIsland-bedfile: ''
+  # Gene annotation, should be refGenes or knownGenes table
+  refGenes-bedfile: ''
 
 general:
   assembly: ''
@@ -36,11 +41,6 @@ general:
     cores: 1
     qvalue: 0.01
     difference: 25
-    annotation:
-      cpgIsland-bedfile: ''
-      refGenes-bedfile: ''
-      # download cpgIsland-bedfile or refGenes-bedfile automatically if not given?
-      webfetch:   no
 
 # DManalyses:
 #   # The names of analyses can be anything but they have to be unique

diff --git a/tests/settings.yaml b/tests/settings.yaml
@@ -2,6 +2,8 @@ locations:
   input-dir: in/
   output-dir: out/
   genome-fasta: genome/sample.fasta
+  cpgIsland-bedfile: genome/cpgIslandExt.hg19.bed.gz
+  refGenes-bedfile: genome/refGene.hg19.bed.gz
 
 general:
   assembly: hg19
@@ -16,9 +18,7 @@ general:
     cores: 1
     qvalue: 0.05
     annotation:
-      cpgIsland-bedfile: pigx_work/refGenome/cpgIslandExt.hg19.bed.gz 
-      refGenes-bedfile: pigx_work/refGenome/refGene.hg19.bed.gz
-      webfetch:   no
+      webfetch: no
 
 DManalyses:
   # The names of analyses can be anything but they have to be unique