Commit c69ae6bf authored by Gerald Salin's avatar Gerald Salin
Browse files

add max_insert_size argument + modified number of threads from 8 to 4, as 8...

add max_insert_size argument + modified number of threads from 8 to 4, as 8 cores are booked in sge and bismark launches 2 instances of bowtie2 with -p 4
parent a641f0b6
......@@ -31,7 +31,7 @@ from string import replace
class Bismark (Analysis):
def define_parameters(self, reference_genome, read1, read2=None, non_directional = False, bowtie2 = False, alignment_mismatch=1):
def define_parameters(self, reference_genome, read1, read2=None, non_directional = False, bowtie2 = False, alignment_mismatch=1, max_insert_size=500):
self.reference_genome = reference_genome
self.reference_directory = os.path.dirname(reference_genome)
self.read1 = InputFileList(read1, Formats.FASTQ)
......@@ -44,8 +44,8 @@ class Bismark (Analysis):
self.output_sorted_bam = OutputFileList(self.get_outputs('{basename_woext}.bam', base_output_names), Formats.BAM)
self.read2=None
#TO DO NB Processor -p
self.args = "--bam -q -p 8 -N " + str(alignment_mismatch)
#TODO NB Processor -p
self.args = "--bam -q -p 4 -N " + str(alignment_mismatch) + " --maxins " + str(max_insert_size)
#TODO : nom des output OK si bowtie2, si bowtie1 {basename}_bismark_pe.bam et {basename}_bismark_PE_report.txt?
if read2:
self.output_bam = OutputFileList(self.get_outputs('{basename}_bismark_bt2_pe.bam', read1), Formats.BAM)
......
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