Commit c16792e0 authored by aknecht2's avatar aknecht2
Browse files

Updated config to add necessary file types for ccat.

parent 9cc3add1
...@@ -28,12 +28,13 @@ align_tools = [ ...@@ -28,12 +28,13 @@ align_tools = [
"bowtie2" "bowtie2"
] ]
# Current peak callign tools # Current peak calling tools
peak_tools = [ peak_tools = [
"spp", "spp",
"macs2", "macs2",
"gem", "gem",
"jamm" "jamm",
"ccat"
] ]
# File extensions # File extensions
...@@ -43,7 +44,7 @@ file_extensions = { ...@@ -43,7 +44,7 @@ file_extensions = {
"sai": ["sai"], "sai": ["sai"],
"sam": ["sam"], "sam": ["sam"],
"bam": ["bam"], "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"], "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
"bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"], "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
"quality": ["quality"], "quality": ["quality"],
...@@ -56,7 +57,9 @@ file_extensions = { ...@@ -56,7 +57,9 @@ file_extensions = {
"txt": ["txt"], "txt": ["txt"],
"chrom_sizes": ["sizes"], "chrom_sizes": ["sizes"],
"read_dist" : ["txt"], "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 # list of resources that can be specified per job (step) in
......
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