Update docs with working examples for manual testing

Author: VerbalCant

docs/development/manual_tests.md

@@ -1136,16 +1136,14 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ --convert_
 
 ### MTDNA HAPLOGROUP CLASSIFICATION
 
-#### ALAINA TODO: ADD SOMETHING HERE
-
 ```bash
 #### MTDNA HAPLOGROUP CLASSIFICATION with default settings
 ## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
 ## Expect: The haplogroup .txt file contains at minimum columns for rank, name, quality, range, and details of the haplogroup assignment
-nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test --run_mtdna_haplogroup -resume
+nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test --run_classify_mtdna_haplogroup --run_genotyping --genotyping_tool ug --genotyping_source raw -resume
 
 #### MTDNA HAPLOGROUP CLASSIFICATION with specific arguments
 ## Expect: Directory created 'mtdna_haplogroup/<reference>/<sample_id>' containing a .txt file for each sample with haplogroup assignments
 ## Expect: The haplogroup assignment may differ based on the classification settings
-nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test_args --run_mtdna_haplogroup --haplogrep_args '--extend-report' -resume
+nextflow run main.nf -profile docker,test --outdir ./results/mtdna_haplogroup_test --run_classify_mtdna_haplogroup --run_genotyping --genotyping_tool ug --genotyping_source raw --haplogrep3_tree_id phylotree-fu-rcrs@1.2 -resume
 ```