Update README.md

Author: evelyn-schmidt

README.md

@@ -171,7 +171,7 @@ Open colored_peptides51mer.html and copy the table into an excel spreadsheet. Th
 
 ## Get Basic QC
 
-```bash
+```
 python3  /opt/scripts/get_neoantigen_qc.py --help
 usage: get_neoantigen_qc.py [-h] [-WB WB] [-f FIN_RESULTS] [--n_dna N_DNA] [--t_dna T_DNA] [--t_rna T_RNA] [--concordance CONCORDANCE] [--contam_n CONTAM_N] [--contam_t CONTAM_T]
                             [--rna_metrics RNA_METRICS] [--strand_check STRAND_CHECK] --yaml YAML [--fin_variants FIN_VARIANTS]
@@ -198,7 +198,7 @@ optional arguments:
 
 ## GET FDA metrics
 
-```bash
+```
 python3  /opt/scripts/get_FDA_thresholds.py --help
 usage: get_FDA_thresholds.py [-h] [-WB WB] [-f FIN_RESULTS] [--n_dna N_DNA] [--t_dna T_DNA] [--t_rna T_RNA] [--una_n_dna UNA_N_DNA] [--una_t_dna UNA_T_DNA] [--una_t_rna UNA_T_RNA]
                              [--somalier SOMALIER] [--contam_n CONTAM_N] [--contam_t CONTAM_T]
@@ -228,7 +228,7 @@ optional arguments:
 
 The set up review script runs two other scripts: generate_reviews_files.py and color_peptides51mer.py. The first sets up the Annotated.Neoantige.Canidates spreadsheet and the Peptides 51mer spreadsheet. The second script colors the Peptides 51mer sequences and outputs an html table whihc can be copied into a Microsoft spreadsheet.
 
-```bash
+```
 python3  /opt/scripts/setup_review.py --help
 usage: setup_review.py [-h] [-WB WB] [-samp SAMP] [-a A] [-c C] -classI CLASSI -classII CLASSII
 
@@ -247,7 +247,7 @@ optional arguments:
 
 ## Generate Review Files
 
-```bash
+```
 python3  /opt/scripts/generate_reviews_files.py --help
 usage: generate_reviews_files.py [-h] [-a A] [-c C] [-samp SAMP] [-WB WB] [-f FIN_RESULTS]
 
@@ -297,7 +297,7 @@ optional arguments:
 
 Bold Class II is not utilized in the current workflow of setting up the manual review. However, it is included as an example of how adding stylization (in this case bold) to certain characters within individual cells of spreadsheets can be accomplished using BeautifulSoup. If you wanted to only bold certain characters (or do any stylzing such as coloring), you can insert a style tag directly into the HTML. However, if you wanted to do formatting inside formatting such as in these review files where there needs to some characters which are red, bold, underlined, or any combination if thise mentioned, BeuaitfulSoup cannot accomplish this. 
 
-```bash
+```
 python3 /opt/scripts/bold_classII.py --help
 usage: bold_classII.py [-h] -p P -classI CLASSI -classII CLASSII -o O