Pipelines¶
Test Tool¶
This is a demonstration pipeline using the testTool.
Running from the command line¶
Parameters¶
- config : file
- Location of the config file for the workflow
- in_metadata : file
- Location of the input list of files required by the process
- out_metadata : file
- Location of the output results.json file for returned files
Returns¶
- output : file
- Text file with a single entry
Example¶
When using a local verion of the [COMPS virtual machine](http://www.bsc.es/computer-sciences/grid-computing/comp-superscalar/downloads-and-documentation):
1 2 | cd /home/compss/code/mg-process-macs2
runcompss --lang=python process_masc2.py --config /home/compss/code/mg-process-macs2/tool_config/process_test.json --in_metadata /home/compss/code/mg-process-macs2/tests/json/input_test.json --out_metadata /home/compss/code/mg-process-macs2/tests/results.json
|
Methods¶
-
class
process_macs2.process_macs2(configuration=None)[source]¶ Functions for demonstrating the pipeline set up.
-
run(input_files, metadata, output_files)[source]¶ Main run function for processing a test file.
Parameters: - input_files (dict) – Dictionary of file locations
- metadata (list) – Required meta data
- output_files (dict) – Locations of the output files to be returned by the pipeline
Returns: - output_files (dict) – Locations for the output txt
- output_metadata (dict) – Matching metadata for each of the files
-