reactivate insertsize

workflows/components/insertssizes.py

@@ -16,6 +16,8 @@
 #
 
 import os,re,pickle
+import logging
+
 from subprocess import Popen, PIPE
 
 from ng6.analysis import Analysis

workflows/methylseq/__init__.py

@@ -129,7 +129,7 @@ class Methylseq (CasavaNG6Workflow):
 #                 parent_for_next_step = rmDuplicate
 
             # process insert sizes of the aligned reads
-            #insertssizesReference = self.add_component("InsertsSizes", [bam_for_next_step, self.histogram_width, self.min_pct, "LENIENT", "inserts_sizes.tar.gz"], component_prefix="paired", parent = parent_for_next_step)
+            insertssizesReference = self.add_component("InsertsSizes", [bam_for_next_step, self.histogram_width, self.min_pct, "LENIENT", "inserts_sizes.tar.gz"], component_prefix="paired", parent = parent_for_next_step)
             # compute the methylation extraction from the alignement
             bismarkReference_extract = self.add_component("BismarkMethylationExtractor", [indexed_ref, bam_for_next_step, "paired" , self.methylation_extractor_no_overlap, self.large_genome], component_prefix="paired",parent = parent_for_next_step)
         else:
@@ -166,7 +166,7 @@ class Methylseq (CasavaNG6Workflow):
 #                     bam_for_next_step = rmDuplicate.output
 #                     parent_for_next_step = rmDuplicate
                 # process insert sizes of the aligned reads
-                #insertssizesControl = self.add_component("InsertsSizes", [bam_for_next_step, insert_size_histogram_width, insert_size_min_percentage, "LENIENT", "inserts_sizes.tar.gz"], component_prefix="control_paired", parent = parent_for_next_step)
+                insertssizesControl = self.add_component("InsertsSizes", [bam_for_next_step, insert_size_histogram_width, insert_size_min_percentage, "LENIENT", "inserts_sizes.tar.gz"], component_prefix="control_paired", parent = parent_for_next_step)
                 # compute the methylation extraction from the alignement
                 bismarkControl_extract = self.add_component("BismarkMethylationExtractor", [indexed_control, bam_for_next_step, "paired" , self.methylation_extractor_no_overlap], component_prefix="control_paired", parent = parent_for_next_step)
             else: