Added peak types for validation, updated run to validated based on info in configuration.

chipathlon/conf.py

@@ -39,6 +39,15 @@ peak_tools = [
     "ccat"
 ]
 
+# Peak_type validation
+peak_types = {
+    "spp": ["narrow", "broad"],
+    "macs2": ["narrow", "broad"],
+    "gem": ["narrow"],
+    "peakranger": ["narrow"],
+    "ccat": ["broad"]
+}
+
 # File extensions
 file_extensions = {
     "genome_index": ["fa", "fna"],
@@ -46,7 +55,7 @@ file_extensions = {
     "sai": ["sai"],
     "sam": ["sam"],
     "bam": ["bam"],
-    "bed": ["bed", "peak", "region", "narrowPeak", "broadPeak", "tagAlign", "narrowPeak.gz"],
+    "bed": ["bed", "peak", "region", "narrowPeak", "broadPeak", "tagAlign", "narrowPeak.gz", "broadPeak.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"],
@@ -139,7 +148,3 @@ genomes = {
         "additional_files": file_extensions["bowtie2_genome"]
     }
 }
-
-# number of lines from BED and peak result files to
-# include per-document for bed and peak collections
-result_lines_per_document = 75000

chipathlon/run.py

@@ -52,11 +52,9 @@ class Run(object):
     def _validate(self):
         if self.peak not in chipathlon.conf.peak_tools:
             self.errors.append("Run defined by %s is invalid.  Specified peak tool is not supported." % (self,))
-        if self.peak_type in ["narrow", "broad"]:
-            if self.peak_type == "broad" and self.peak not in ["spp", "macs2", "peakranger"]:
-                self.errors.append("Run defined by %s is invalid.  Specified peak calling type '%s' is invalid with peak calling tool '%s'." % (self, self.peak_type, self.peak))
         else:
-            self.errors.append("Run defined by %s is invalid.  Specified peak calling type '%s' is not supported." % (self, self.peak_type))
+            if self.peak_type not in chipathlon.conf.peak_types[self.peak]:
+                self.errors.append("Run defined by %s is invalid.  Specified peak calling type '%s' is invalid with peak calling tool '%s'.  Should be one of %s." % (self, self.peak_type, self.peak, chipathlon.conf.peak_types[self.peak]))
         if self.idr is not None:
             if len(self.signals) >= 2:
                 if len(self.idr) == 2: