Develop

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

Resolve "MultiQC error"

Closes #36

See merge request !56

Remove md changes from CI

See merge request !55

Resolve "Add cellranger v 3.1.0"

Closes #30, #31, #32, and #33

See merge request !54