update docs

Author: kcotto

docs/workflow.md

@@ -119,10 +119,10 @@ Sample_2
 **`tumor_rna_alignments.bam.bai`** - index file for the above RNA-seq alignment file.\
 **`variants.vcf.gz`** - a compressed vcf file containing all variants from a given samples.\
 **`variants.vcf.gz.tbi`** - an index file for the vcf file mentioned above.\
-**`logs/`** - directory containing log or error files for a given sample.
-**`output/`** - directory containing RegTools output files for a given sample.
-**`cse_identify_filtered_*`** - RegTools output files from the initial RegTools run for a given sample. This will contain results for this sample's variants only.
-**`cse_identify_filtered_compare_*`** - RegTools output files from the second RegTools run for a given sample. This will contain results for all samples' variants.
-**`variants*.bed`** - a bedfile containing the variants considered to be splicing relevant for a given RegTools parameter. This is used later to make `all_splicing_variants*.bed`.
-**`compare_junctions/hist/`** - directory containing output from the statistics script analyze all variants across all samples.
+**`logs/`** - directory containing log or error files for a given sample.\
+**`output/`** - directory containing RegTools output files for a given sample.\
+**`cse_identify_filtered_*`** - RegTools output files from the initial RegTools run for a given sample. This will contain results for this sample's variants only.\
+**`cse_identify_filtered_compare_*`** - RegTools output files from the second RegTools run for a given sample. This will contain results for all samples' variants.\
+**`variants*.bed`** - a bedfile containing the variants considered to be splicing relevant for a given RegTools parameter. This is used later to make `all_splicing_variants*.bed`.\
+**`compare_junctions/hist/`** - directory containing output from the statistics script analyze all variants across all samples.\
 **`junction_pvalues_*.tsv`** - a file containing the output from the statistic analysis script.