Commit 1d021861 authored by Celine Noirot's avatar Celine Noirot
Browse files

Set bismark CPU and Memory variable

parent 8f2d3fa4
......@@ -27,7 +27,8 @@ from ng6.utils import Utils
#TODO : not tested in single-end mode
#TODO : max insert size for bismark not yet managed
class Methylseq (CasavaNG6Workflow):
BISMARK_CPU=8
BISMARK_RAM=8G
def get_name(self):
return 'methylseq'
......@@ -57,8 +58,7 @@ class Methylseq (CasavaNG6Workflow):
def process(self):
fastqilluminafilter, filtered_read1_files, filtered_read2_files, concat_files = self.illumina_process()
# handle if run name have spaces
run_name = "_".join(self.runobj.name.split())
......@@ -111,8 +111,9 @@ class Methylseq (CasavaNG6Workflow):
bam_for_next_step = bismarkReference.output_bam
parent_for_next_step = bismarkReference
if not self.rrbs :
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkReference.output_bam,self.is_paired_end()], component_prefix="paired",parent = bismarkReference)
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkReference.output_bam,self.is_paired_end(),BISMARK_RAM,BISMARK_CPU], component_prefix="paired",parent = bismarkReference)
bam_for_next_step = rmDuplicate.output
print("RMDUP" , bam_for_next_step)
parent_for_next_step = rmDuplicate
# process insert sizes of the aligned reads
......@@ -125,7 +126,7 @@ class Methylseq (CasavaNG6Workflow):
bam_for_next_step = bismarkReference.output_bam
parent_for_next_step = bismarkReference
if not self.rrbs :
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkReference.output_bam,self.is_paired_end()], component_prefix="paired",parent = bismarkReference)
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkReference.output_bam,self.is_paired_end(),BISMARK_RAM,BISMARK_CPU], component_prefix="paired",parent = bismarkReference)
bam_for_next_step = rmDuplicate.output
parent_for_next_step = rmDuplicate
# compute the methylation extraction from the alignement
......@@ -146,7 +147,7 @@ class Methylseq (CasavaNG6Workflow):
parent_for_next_step = bismarkControl
if not self.rrbs :
#remove duplicate
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkControl.output_bam,self.is_paired_end()], component_prefix="control_paired",parent = bismarkControl)
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkControl.output_bam,self.is_paired_end(),BISMARK_RAM,BISMARK_CPU], component_prefix="control_paired",parent = bismarkControl)
bam_for_next_step = rmDuplicate.output
parent_for_next_step = rmDuplicate
# process insert sizes of the aligned reads
......@@ -160,7 +161,7 @@ class Methylseq (CasavaNG6Workflow):
parent_for_next_step = bismarkControl
if not self.rrbs :
#remove duplicate
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkControl.output_bam,self.is_paired_end()], component_prefix="control",parent = bismarkControl)
rmDuplicate = self.add_component("RemoveDuplicate", [bismarkControl.output_bam,self.is_paired_end(),BISMARK_RAM,BISMARK_CPU], component_prefix="control",parent = bismarkControl)
bam_for_next_step = rmDuplicate.output
parent_for_next_step = rmDuplicate
# compute the methylation extraction from the alignement
......
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