Merge pull request #24 from wslh-bio/dev-update-final-report

Dev update final report

Merge pull request #23 from wslh-bio/dev-read-repair

Merge pull request #22 from wslh-bio/dev-calcassemblyratio-fix

Merge pull request #21 from wslh-bio/bug-handle-missing-species-in-as…

…sembly-stats

Bug fix: Handling of Missing Species in NCBI Assembly Stats and GC Content Outputs

Merge pull request #20 from wslh-bio/bug-noscheme-mlst-output

Fix 'NoScheme Available' bug by detecting '-' in MLST file instead of…

Merge pull request #19 from wslh-bio/dev-mlst-output-update

Dev mlst output update

Merge pull request #18 from wslh-bio/dev-retry-and-ignore

Dev retry and ignore

Merge pull request #17 from wslh-bio/dev-schema-fix

Dev schema fix

Merge pull request #16 from wslh-bio/dev-calculate_ncbi_stats

Dev calculate ncbi stats

Add --plus for no --organism option