Commit 70df192a authored by Gerald Salin's avatar Gerald Salin
Browse files

full arg list + err output redirect

parent 399e2cb6
......@@ -49,13 +49,13 @@ class BismarkMethylationExtractor (Analysis):
if type == "single" :
self.args += " --single-end"
#self.args += " --report --bedGraph --counts --cytosine_report --zero_based --CX_context --buffer_size 8G"
self.args += " --report --buffer_size 8G"
self.args += " --report --bedGraph --counts --cytosine_report --zero_based --CX_context --buffer_size 8G"
#self.args += " --report --buffer_size 8G"
logging.getLogger("BismarkMethylationExtractor.define_parameters").debug("Leaving")
def process(self):
bismark_extract = ShellFunction("mkdir $2; cd $2; " + self.get_exec_path("samtools") + " sort -n $1 $1; rm $1; mv $1.bam $1;" + self.get_exec_path("bismark_methylation_extractor") + " $1 " + self.args + \
" --genome_folder " + os.path.dirname(self.reference_genome) + " -o $2 2> $3; " + self.get_exec_path("samtools") + " sort $1 $1; rm $1; mv $1.bam $1;", cmd_format='{EXE} {IN} {OUT}')
" --genome_folder " + os.path.dirname(self.reference_genome) + " -o $2 2>> $3; " + self.get_exec_path("samtools") + " sort $1 $1 2>> $3; rm $1; mv $1.bam $1 2>> $3;", cmd_format='{EXE} {IN} {OUT}')
bismark_map = MultiMap(bismark_extract, inputs=self.bams, outputs=[self.output_directories,self.stderrs], includes=self.reference_genome)
def define_analysis(self):
......
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