process_fastqc.py

#!/usr/bin/env python

"""
.. See the NOTICE file distributed with this work for additional information
   regarding copyright ownership.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
"""
from __future__ import print_function

import argparse

from basic_modules.workflow import Workflow
from utils import logger

from tool.validate_fastqc import fastqcTool


# ------------------------------------------------------------------------------

class process_fastqc(Workflow):
    """
    Workflow to download and pre-index a given genome
    """

    def __init__(self, configuration=None):
        """
        Initialise the class

        Parameters
        ----------
        configuration : dict
            a dictionary containing parameters that define how the operation
            should be carried out, which are specific to each Tool.
        """
        logger.info("Validationing FastQ file")
        if configuration is None:
            configuration = {}

        self.configuration.update(configuration)

    def run(self, input_files, metadata, output_files):  # pylint: disable=no-self-use
        """
        Main run function for the validation of FASTQ files. The pipeline uses FastQC

        Parameters
        ----------
        input_files : dict
            fastq : str
                List of file locations
        metadata : dict
            fastq : dict
                Required meta data
        output_files : dict
            report : str
                Location of the HTML

        Returns
        -------
        outputfiles : dict
            List of locations for the output index files
        output_metadata : dict
            Metadata about each of the files
        """

        output_files_generated = {}
        output_metadata = {}

        # FastQC Validation
        logger.info("Generating validation report for FastQ file")
        fastqc_handle = fastqcTool()
        logger.progress("FASTQC Validation", status="RUNNING")
        bti, btm = fastqc_handle.run(
            input_files,
            metadata,
            {'report': output_files['report']}
        )
        logger.progress("FASTQC Validation", status="DONE")

        try:
            output_files_generated['report'] = bti["report"]
            output_metadata['report'] = btm['report']

            tool_name = output_metadata['report'].meta_data['tool']
            output_metadata['report'].meta_data['tool_description'] = tool_name
            output_metadata['report'].meta_data['tool'] = "process_fastqc"
        except KeyError:
            logger.fatal("FastQ validation process failed")

        return (output_files_generated, output_metadata)


# ------------------------------------------------------------------------------

def main_json(config, in_metadata, out_metadata):
    """
    Alternative main function
    -------------

    This function launches the app using configuration written in
    two json files: config.json and input_metadata.json.
    """
    # 1. Instantiate and launch the App
    logger.info("1. Instantiate and launch the App")
    from apps.jsonapp import JSONApp
    app = JSONApp()
    result = app.launch(process_fastqc,
                        config,
                        in_metadata,
                        out_metadata)

    # 2. The App has finished
    logger.info("2. Execution finished; see " + out_metadata)

    return result


# ------------------------------------------------------------------------------

if __name__ == "__main__":

    # Set up the command line parameters
    PARSER = argparse.ArgumentParser(description="Validate FastQ file")
    PARSER.add_argument(
        "--config", help="Configuration file")
    PARSER.add_argument(
        "--in_metadata", help="Location of input metadata file")
    PARSER.add_argument(
        "--out_metadata", help="Location of output metadata file")
    PARSER.add_argument(
        "--local", action="store_const", const=True, default=False)

    # Get the matching parameters from the command line
    ARGS = PARSER.parse_args()

    CONFIG = ARGS.config
    IN_METADATA = ARGS.in_metadata
    OUT_METADATA = ARGS.out_metadata
    LOCAL = ARGS.local

    if LOCAL:
        import sys
        sys._run_from_cmdl = True  # pylint: disable=protected-access

    RESULTS = main_json(CONFIG, IN_METADATA, OUT_METADATA)
    print(RESULTS)