📖 add secondary file note

Author: migbro

readme.md

@@ -26,10 +26,9 @@ this can be used later on for further analysis in joint trio genotyping and subs
 ## Inputs:
 ```yaml
   input_bam: input.bam
-  reference_fasta: Homo_sapiens_assembly38.fasta
+  reference_fasta: Homo_sapiens_assembly38.fasta # For proper bwa functionality, you also need to copy over all bwa index files related to this reference, with suffixes .alt, .amb, .ann, .bwt, .pac, .sa.  These are known as "secondary files" in cwl.
   reference_fai: Homo_sapiens_assembly38.fai
   reference_dict: Homo_sapiens_assembly38.dict
-  bwa_index_tar: Homo_sapiens_assembly38.fasta.bwa-0.7.17.tar # tar ball with genome fasta file and all bwa index files
   knownsites:
   - 1000G_omni2.5.hg38.vcf.gz
   - 1000G_phase1.snps.high_confidence.hg38.vcf.gz
@@ -47,4 +46,6 @@ this can be used later on for further analysis in joint trio genotyping and subs
 - [sequence_grouping_tsv](examples/sequence_grouping.txt), generated by `bin/CreateSequenceGroupingTSV.py`
 - [example-inputs.json](examples/example-inputs.json)
 
+Note, for all vcf files, indexing may be required - a "secondary file" requirement.
+
 ![WF Visualized](./kfdrc_alignment_wf.png?raw=true "Workflow diagram")