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()
bti, btm = fastqc_handle.run(
input_files,
metadata,
{'report': output_files['report']}
)
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 test_fastqc_hic_1():
"""
Test case to ensure that the GEM indexer works.
"""
resource_path = os.path.join(os.path.dirname(__file__), "data/")
input_files = {"fastq": resource_path + "tb.Human.SRR1658573_2.fastq.gz"}
output_files = {
"report": resource_path + "tb.Human.SRR1658573_2.report",
}
metadata = {
"fastq": Metadata("data_rnaseq", "fastq", [], None,
{'assembly': 'test'})
}
fastqc_handle = fastqcTool()
fastqc_handle.run(input_files, metadata, output_files)
assert os.path.isfile(output_files["report"]) is True
assert os.path.getsize(output_files["report"]) > 0
