radpipe/stages.py
def bwa_index(self, input, outputs, reference_dir):
        '''Index reference genome for bwa alignment'''
        safe_make_dir(reference_dir)
        command = "ln -sf {ref_fasta} {ref_symlink} && bwa index {ref_symlink}".format(
                      ref_fasta=os.path.abspath(input),
                      ref_symlink=os.path.join(reference_dir, "reference.fa"))
        run_stage(self.state, "build_index", command)
Index reference genome for bwa alignment
Index reference genome for bwa alignment
Index reference genome for bwa alignment
def bwa_index(self, input, outputs, reference_dir):
        safe_make_dir(reference_dir)
        command = "ln -sf {ref_fasta} {ref_symlink} && bwa index {ref_symlink}".format(
                      ref_fasta=os.path.abspath(input),
                      ref_symlink=os.path.join(reference_dir, "reference.fa"))
        run_stage(self.state, "build_index", command)
def bwa_index ( self , input , outputs , reference_dir ) : safe_make_dir ( reference_dir ) command = "ln -sf {ref_fasta} {ref_symlink} && bwa index {ref_symlink}" . format ( ref_fasta = os . path . abspath ( input ) , ref_symlink = os . path . join ( reference_dir , "reference.fa" ) ) run_stage ( self . state , "build_index" , command )
Index reference genome for bwa alignment
Index reference genome for bwa alignment
'''Index reference genome for bwa alignment'''
self
input
outputs
reference_dir