Update workflow/main.nf, workflow/scripts/check_design.py,...

Update workflow/main.nf, workflow/scripts/check_design.py, workflow/scripts/generate_references.py, workflow/scripts/generate_versions.py, workflow/scripts/filename_check.sh, workflow/tests/test_check_design.py, workflow/tests/test_count.py, workflow/tests/test_multiqc.py, workflow/tests/test_versions.py files