Commit 8e577650 authored by Celine Noirot's avatar Celine Noirot
Browse files

debug save correct files in bismark instead of bismark_methylation_extractor.

parent f7490e26
......@@ -124,6 +124,7 @@ class Bismark (Analysis):
bismark_map = MultiMap(bismark_fn, self.input_files_R1, outputs=[self.output_files,self.stderrs,self.output_report,self.output_bam], includes=self.reference_genome)
def post_process(self):
self._save_files(self.output_bam)
results_files = self.output_report
# Finally create and add the archive to the analysis
for file in self.output_report:
......@@ -175,7 +176,6 @@ class Bismark (Analysis):
@return : {"nbseq" : x, ...}
"""
stats = {}
for line in open(report_file, 'r').readlines():
#if paired
if line.startswith("Sequence pairs analysed in total:"):
......
......@@ -63,10 +63,7 @@ class BismarkMethylationExtractor (Analysis):
def post_process(self):
# save sorted bam in bismark analysis
bismark_analysis = Analysis.get_from_id(self.parent.id)
bismark_analysis._save_files(self.bams)
for directory in self.output_directories :
methylationExtractorResultFiles = []
sample = os.path.basename(directory)
......
......@@ -58,7 +58,7 @@ class RemoveDuplicate (Analysis):
else :
self.options +=" -s |samtools flagstat"
def get_version(self):
cmd = [self.get_exec_path("samtools")]
cmd = [self.get_exec_path("samtools_old")]
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
return str(stderr).split("\\n")[2].replace("Version: ","")
......
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