Apply suggestions from code review

Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>

docs/STAR_2.7.11b_DIPLOID.md

@@ -11,16 +11,16 @@ The STAR Diploid mode has a known bug with an unknown cause manifests as a seg f
 ## Introduction
 This pipeline runs the following steps:
 1. STAR Genome Generate per individual, or will skip if one has been generated already.
-    -  Strip existing annotations as defined by the user. Since STAR requires an uncompressed vcf, this helps make the input file size smaller as only variant calls and `FORMAT` info are needed
+    -  Strip existing annotations as defined by the user. Since STAR requires an uncompressed VCF, this helps make the input file size smaller as only variant calls and `FORMAT` info are needed
     -  Filtering steps for input patient DNA variant calls in order to focus on higher quality calls.
     Recommended filtering criteria recommendations are still being established, but various scenarios and suggestions from our and partner institutions can be found in the inputs section.
-    - Use a genome fasta and gtf - recommend fasta matches input DNA calls - in conjunction with filtered DNA VCF to create PG
-1. If needed, convert input bam reads to fastq
-1. If needed, cutadapt to remove any adapters
+    - Use a genome FASTA and GTF - recommend FASTA matches input DNA calls - in conjunction with filtered DNA VCF to create PG
+1. If needed, convert input BAM reads to FASTQ
+1. If needed, Cutadapt to remove any adapters
 1. Run STAR aligner 
     - Use PG as refs
     - Align input reads
-1. Run custom tool to filter bam for RSEM. Removes indels and soft-clipped reads
+1. Run custom tool to filter BAM for RSEM. Removes indels and soft-clipped reads
 1. RSEM quantification
 
 ### Cutadapt
@@ -70,7 +70,7 @@ If a pre-existing PG does not exist, need the following inputs to create:
 
 ## Filtering and Input Appendix
 ### Input creation
- - `genome_fa` was generated by first downloading the [complete hg38 fasta](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta) from Broad, then creating a chr1-22,X,Y,M chromosome list, and running the following commands to get the fasta file and index: 
+ - `genome_fa` was generated by first downloading the [complete hg38 FASTA](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta) from Broad, then creating a chr1-22,X,Y,M chromosome list, and running the following commands to get the FASTA file and index: 
    ```sh
    samtools faidx Homo_sapiens_assembly38.fasta -r chr_list.txt > Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta
    samtools faidx Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta

tools/star_2.7.11b_personal_genome_generate.cwl

@@ -2,7 +2,7 @@ cwlVersion: v1.2
 class: CommandLineTool
 id: star_2-7-11a_build_personal_ref
 label: "STAR Personal Reference Genome Index Generator"
-doc: " Allow user to create a custom genome to align aganist"
+doc: "Allow user to create a custom genome to align against"
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement
@@ -12,12 +12,12 @@ requirements:
     coresMin: $(inputs.runThreadN)
     ramMin: ${ return inputs.memory * 1000 }
 
-baseCommand: [mkdir]
+baseCommand: []
 arguments:
   - position: 1
     shellQuote: false
     valueFrom: >-
-      $(inputs.genomeDir)
+      mkdir $(inputs.genomeDir)
   - position: 2
     shellQuote: false
     valueFrom: >-