Move the code for the bin/run_qc.py standalone QC pipeline runner utility into a submodule auto_process_ngs/cli/run_qc.py, and refactor some of the internal functionality into functions (previously it was essentially one monolithic __main__ process).
Some deprecated options have also been dropped completely, and the --fastq_screen_subset option has been replaced by the --fastq_subset option.
Move the code for the
bin/run_qc.pystandalone QC pipeline runner utility into a submoduleauto_process_ngs/cli/run_qc.py, and refactor some of the internal functionality into functions (previously it was essentially one monolithic__main__process).Some deprecated options have also been dropped completely, and the
--fastq_screen_subsetoption has been replaced by the--fastq_subsetoption.