Auto Generate Output File Locations

[markmcdowall]

At the moment the location of the output files and the names of the files need to be specified in the config.json file. From the VRE perspective that can mean that the names are very bland and difficult to use when files have the same name and visualising this in JBrowse.

This needs a small change in the pipelines to add a test for if the name has been generated already, if not then auto-generate the name based on the execution parameter and the name of the input file.

tool_output_list = {}
if output_files["output_file_1"]:
    tool_output_list["output_file_1"] = output_files["output_file_1"]
else:
    tool_output_list["output_file_1"] = os.path.join(
        self.configuration["execution"],
        input_files["input_file_1"].replace("fastq", "bam")
    )

This will need to be done at the pipeline/workflow level as it is at this level that the management of files is performed. Tools should not define the output files.