update docs

Author: kcotto

docs/workflow.md

@@ -103,26 +103,26 @@ Rscript --vanilla filter_and_BH.R <tag>
 
 ## File description
 
-**`all_splicing_variants*.bed`** - a file containing all of the variants that regtools identified as being associated with a junction for the given parameters used to run `cis-splice-effects identify`.\
-**`dir_names.tsv`** - a file containing a list of each of the sample directories with each directory on a new line. This can be obtained by using `ls samples/ > dir_names.tsv`. For this example, it would look like:
+* **`all_splicing_variants*.bed`** - a file containing all of the variants that regtools identified as being associated with a junction for the given parameters used to run `cis-splice-effects identify`.
+* **`dir_names.tsv`** - a file containing a list of each of the sample directories with each directory on a new line. This can be obtained by using `ls samples/ > dir_names.tsv`. For this example, it would look like:
 
 ```bash
 Sample_1
 Sample_2
 ```
 
-**`variants_all_sorted.vcf.gz`** - a compressed vcf file containing all variants from all samples.\
-**`variants_all_sorted.vcf.gz.tbi`** - an index file for the vcf file mentioned above.\
-**`samples/`** - a directory containing each of the samples to be analyzed alongside each other.\
-**`Sample_1/`** - a sample directory. This will contain input data files as well as output files from RegTools.\
-**`tumor_rna_alignments.bam`** - file containing aligned RNA-seq reads for the given sample.\
-**`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.\
-**`junction_pvalues_*.tsv`** - a file containing the output from the statistic analysis script.
+* **`variants_all_sorted.vcf.gz`** - a compressed vcf file containing all variants from all samples.
+* **`variants_all_sorted.vcf.gz.tbi`** - an index file for the vcf file mentioned above.
+* **`samples/`** - a directory containing each of the samples to be analyzed alongside each other.
+* **`Sample_1/`** - a sample directory. This will contain input data files as well as output files from RegTools.
+* **`tumor_rna_alignments.bam`** - file containing aligned RNA-seq reads for the given sample.
+* **`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.
+* **`junction_pvalues_*.tsv`** - a file containing the output from the statistic analysis script.