def execute(self, run_id, run):
with process_pool.ProcessPool(self) as pool:
with pool.Pipeline(pool) as pipeline:
## Append the input files, which are all input file linked to the output file
item_A_path = run.get_private_info('features_segemehl_path')
item_B_path = run.get_private_info('features_tophat_path')
## Obtain the output files
gtf_out_path = run.get_single_output_file_for_annotation('features')
## Call Rscript
rscript = [self.get_tool('Rscript'), self.get_option('path_rscript')]
## Append input files
rscript.extend (['--inputA', item_A_path])
rscript.extend (['--inputB', item_B_path])
## Append the output files
rscript.extend (['--output', gtf_out_path])
## Append prefixes
rscript.extend (['--prefixA', 'segemehl'])
rscript.extend (['--prefixB', 'tophat'])
## Append mode of combining the GTF files
rscript.extend (['--mode', 'no_transcript_overlap'])
log_stderr = run.get_single_output_file_for_annotation('log_stderr')
log_stdout = run.get_single_output_file_for_annotation('log_stdout')
pipeline.append (rscript, stderr_path = log_stderr, stdout_path = log_stdout)
def execute(self, run_id, run):
# process one file at a time
for tag, output_file_info in run.get_output_files_abspath().items():
for output_path, input_paths in output_file_info.items():
with process_pool.ProcessPool(self) as pool:
with pool.Pipeline(pool) as pipeline:
cat = [self.get_tool('cat'), input_paths[0]]
pigz1 = [self.get_tool('pigz'), '--decompress', '--processes', '1', '--stdout']
tool_command = [self.get_tool(self._tool)]
tool_command.extend(self.tool_command_line())
pigz2 = [self.get_tool('pigz'), '--processes', '2', '--blocksize', '4096', '--stdout']
if output_path[-3:] == '.gz':
pipeline.append(cat)
pipeline.append(pigz1)
pipeline.append(tool_command)
pipeline.append(pigz2, stdout_path = output_path)
else:
pipeline.append(cat)
pipeline.append(tool_command, stdout_path = output_path)