Commit 5ab283f6 authored by Gerald Salin's avatar Gerald Salin
Browse files

reactivate insertsize

parent f459dde2
......@@ -16,6 +16,8 @@
#
import os,re,pickle
import logging
from subprocess import Popen, PIPE
from ng6.analysis import Analysis
......
......@@ -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:
......
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