Commit 2578e09c authored by Gerald Salin's avatar Gerald Salin
Browse files

add insertSizes components

parent c69ae6bf
......@@ -137,14 +137,15 @@ class Methylseq (NG6Workflow):
indexed_ref = bismark_genome_preparation.databank_fasta
if is_paired_end :
bismarkReference = self.add_component("Bismark", [indexed_ref,trim_galore.read1_cleaned, trim_galore.read2_cleaned,self.args["non_directional"],self.args["bowtie2"],self.args["alignment_mismatch"]], component_prefix="paired",parent = trim_galore)
insertssizesReference = self.add_component("InsertsSizes", [bismarkReference.output_sorted_bam, self.args["histogram_width"], self.args["min_pct"], "LENIENT", "inserts_sizes.tar.gz"], component_prefix="paired", parent = bismarkReference)
bismarkReference_extract = self.add_component("BismarkMethylationExtractor", [indexed_ref, bismarkReference.output_sorted_bam, "paired" , self.args["methylation_extractor_no_overlap"]], component_prefix="paired",parent = bismarkReference)
# make some statistic on the alignement (disabled due to errors during parsing)
#alignmentstats = self.add_component("AlignmentStats", [bismarkReference.output_sorted_bam, is_paired_end, False], parent = bismarkReference, component_prefix="PEreference")
alignmentstats = self.add_component("AlignmentStats", [bismarkReference.output_sorted_bam, is_paired_end, False], parent = bismarkReference, component_prefix="PEreference")
else:
bismarkReference = self.add_component("Bismark", [indexed_ref,trim_galore.read1_cleaned, None ,self.args["non_directional"],self.args["bowtie2"],self.args["alignment_mismatch"]],parent = trim_galore)
bismarkReference_extract = self.add_component("BismarkMethylationExtractor", [indexed_ref, bismarkReference.output_sorted_bam, "single" , self.args["methylation_extractor_no_overlap"]], parent = bismarkReference)
# make some statistic on the alignement (disabled due to errors during parsing)
#alignmentstats = self.add_component("AlignmentStats", [bismarkReference.output_sorted_bam, is_paired_end, False], parent = bismarkReference, component_prefix="SEreference")
alignmentstats = self.add_component("AlignmentStats", [bismarkReference.output_sorted_bam, is_paired_end, False], parent = bismarkReference, component_prefix="SEreference")
if self.args["control_reference"]:
logging.getLogger("Methylseq").debug("Controle sequence = " + self.args["control_reference"])
......@@ -156,13 +157,14 @@ class Methylseq (NG6Workflow):
if is_paired_end :
bismarkControl = self.add_component("Bismark", [indexed_control,trim_galore.read1_cleaned, trim_galore.read2_cleaned,self.args["non_directional"],self.args["bowtie2"],self.args["alignment_mismatch"]], component_prefix="control_paired", parent = trim_galore)
insertssizesControl = self.add_component("InsertsSizes", [bismarkControl.output_sorted_bam, self.args["histogram_width"], self.args["min_pct"], "LENIENT", "inserts_sizes.tar.gz"], component_prefix="control_paired", parent = bismarkControl)
bismarkControl_extract = self.add_component("BismarkMethylationExtractor", [indexed_control, bismarkControl.output_sorted_bam, "paired" , self.args["methylation_extractor_no_overlap"]], component_prefix="control_paired", parent = bismarkControl)
# make some statistic on the alignement (disabled due to errors during parsing)
#alignmentstats = self.add_component("AlignmentStats", [bismarkControl.output_sorted_bam, is_paired_end, False], parent = bismarkControl, component_prefix="PEcontrol")
alignmentstats = self.add_component("AlignmentStats", [bismarkControl.output_sorted_bam, is_paired_end, False], parent = bismarkControl, component_prefix="PEcontrol")
else:
bismarkControl = self.add_component("Bismark", [indexed_control,trim_galore.read1_cleaned, None ,self.args["non_directional"],self.args["bowtie2"],self.args["alignment_mismatch"]], component_prefix="control", parent = trim_galore)
bismarkControl_extract = self.add_component("BismarkMethylationExtractor", [indexed_control, bismarkControl.output_sorted_bam, "single" , self.args["methylation_extractor_no_overlap"]], component_prefix="control", parent = bismarkControl)
# make some statistic on the alignement (disabled due to errors during parsing)
#alignmentstats = self.add_component("AlignmentStats", [bismarkControl.output_sorted_bam, is_paired_end, False], parent = bismarkControl, component_prefix="SEcontrol")
alignmentstats = self.add_component("AlignmentStats", [bismarkControl.output_sorted_bam, is_paired_end, False], parent = bismarkControl, component_prefix="SEcontrol")
logging.getLogger("Methylseq").debug("Leaving Methylseq pipeline")
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment