Resolve 37-Design File Check

Closes #37

See merge request !58

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

Resolve "Test for kitVersion=3 and version=2.1.1 and exit if true"

Closes #29

See merge request !52

Resolve "Add pytest to CI"

Closes #28

See merge request !51

Merge branch '28-AddPytestCI' of git.biohpc.swmed.edu:BICF/Astrocyte/cellranger_count into 28-AddPytestCI

This reverts commit 798c71d5