Update workflow/scripts/generate_references.py,...

Update workflow/scripts/generate_references.py, workflow/scripts/generate_versions.py, workflow/scripts/versions_fastqc.sh, workflow/tests/test_check_design.py, workflow/scripts/countDesign.sh, workflow/tests/test_fastqc.py, workflow/tests/test_mkfastq.py, workflow/tests/test_multiqc.py, workflow/tests/test_untarBCL.py, workflow/tests/test_versions.py, workflow/scripts/versions_mkfastq.sh, workflow/scripts/untarBCL.sh, workflow/scripts/check_design.py files