Fix formatting

Author: susannasiebert

02-prerequisites.Rmd

@@ -71,6 +71,7 @@ cell line. Data from this cell line is commonly used as test data in bioinformat
 applications. The input data consists of the following files:
 
 For pVACseq:
+
 - `annotated.expression.vcf.gz`: A somatic (tumor-normal) VCF and its tbi index file. The VCF has been
   annotated with VEP and has coverage and expression information added and.
 - `phased.vcf.gz`: A phased tumor-germline VCF and its tbi index file to provide information about
@@ -79,19 +80,20 @@ For pVACseq:
 - `optitype_normal_result.tsv`: A OptiType file with HLA allele typing predictions
 
 For pVACfuse:
+
 - `agfusion_results`: A AGFusion output directory with annotated fusion calls
 - `star-fusion.fusion_predictions.tsv`: A STARFusion prediction file with fusion read support
   and expression information
 
 General:
+
 - `Homo_sapiens.GRCh38.pep.all.fa.gz`: A reference proteome peptide FASTA to use
   for determining whether there are any reference matches of neoantigen candidates
 
 To download this data, please run the following command:
 
 ```{r, engine = 'bash', eval = FALSE}
-wget
-https://raw.githubusercontent.com/griffithlab/pVACtools_Intro_Course/main/HCC1395_inputs.zip
+wget https://raw.githubusercontent.com/griffithlab/pVACtools_Intro_Course/main/HCC1395_inputs.zip
 unzip HCC1395_inputs.zip
 ```