Updated config to add necessary file types for ccat.

chipathlon/conf.py

@@ -28,12 +28,13 @@ align_tools = [
     "bowtie2"
 ]
 
-# Current peak callign tools
+# Current peak calling tools
 peak_tools = [
     "spp",
     "macs2",
     "gem",
-    "jamm"
+    "jamm",
+    "ccat"
 ]
 
 # File extensions
@@ -43,7 +44,7 @@ file_extensions = {
     "sai": ["sai"],
     "sam": ["sam"],
     "bam": ["bam"],
-    "bed": ["bed", "narrowPeak", "broadPeak", "tagAlign", "narrowPeak.gz"],
+    "bed": ["bed", "peak", "region", "narrowPeak", "broadPeak", "tagAlign", "narrowPeak.gz"],
     "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
     "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
     "quality": ["quality"],
@@ -56,7 +57,9 @@ file_extensions = {
     "txt": ["txt"],
     "chrom_sizes": ["sizes"],
     "read_dist" : ["txt"],
-    "plaintext": ["txt", "md"]
+    "plaintext": ["txt", "md"],
+    "ccat_conf": ["txt", "conf"],
+    "log": ["log"]
 }
 
 # list of resources that can be specified per job (step) in