Updating README.md to further explain different inputs.

Arvados-DCO-1.1-Signed-off-by: Alex Coleman <alex.coleman@curii.com>

diff --git a/cwl/gvcf2fasta/README.md b/cwl/gvcf2fasta/README.md
index eaa252bbe00418d0491d6f71c4ae5b7219b98ef4..c995c2da5eaa2afb362ce40d09bc14fb159029c1 100644 (file)
--- a/cwl/gvcf2fasta/README.md
+++ b/cwl/gvcf2fasta/README.md
@@ -9,7 +9,11 @@ This directory contains cwl files and associated shell scripts for converting gV
 Example YAML document can be found under `yml/examplegvcf2fasta.yml`. This is an example for NON-REF workflow.
 ### Building Dockerfile
 The Dockerfile can be found under ../../docker/gvcf2fasta.
-docker build -t vcfutil -f ../../docker/gvcf2fasta/Dockerfile .
+
+The docker image can be built from the current directory using the following command: 
+
+`docker build -t vcfutil -f ../../docker/gvcf2fasta/Dockerfile .`
+
 ### Basic workflow 
 This assumes a straightfoward gVCF (not NON-REF/split/etc).
 #### Inputs needed:
@@ -31,29 +35,32 @@ This is for split VCF files where imputation is required.
 
 #### Additional Inputs needed:
 * **split**: `True`
+* **splitvcfdir** - instead of *vcfdir* or *vcfs*, provide vcfs in the form of a *splitvcfdir*
 * **panelnocallbed**
 * **panelcallbed** 
 * **mapsdir** 
 * **refsdir**
 * **chrs**
-* 
+  
 ### Split VCF/No Imputation workflow
 
 This is the same as above, however imputation is not required.
 
 #### Additional Inputs needed:
 * **split**: `True`
+* **splitvcfdir** - instead of *vcfdir* or *vcfs*, provide vcfs in the form of a *splitvcfdir*
+* Leave out all extra inputs like **chrs**
   
 ### Split VCF/Tar workflow
 
 This is for split and tar files.
 
-#### Inputs needed:
+#### Additional Inputs needed:
 * **split**: `True`
 * **tar**: `True`
 
 
-***NOTE**: at this stage, you have enough information to run the workflow. Below just gives more information about various helper files and subworkflows, for those who are interested.
+**NOTE**: at this stage, you have enough information to run the workflow. Below just gives more information about various helper files and subworkflows, for those who are interested.
 
 The workflow supports many types of inputs: including 
 ## Main workflow
@@ -61,7 +68,7 @@ The workflow supports many types of inputs: including
 The main workflow to run is `maingvcf2fasta.cwl`.
 The main workflow runs gVCF to FASTA workflow with a variety of different inputs/gVCF file formats (split/non-ref/etc). The type of gVCF file provided/type of workflow run influences input parameters.
 
-### Inputs**
+### Inputs
 VCF files can be provided in many different formats, depending on which version of the workflow is run. 
 
 For general workflow type (as well as nonref) either `.gz` or `.vcf` can be provided. However certain workflows require all vcfs to be gzipped. ADD SOME MORE HERE.
@@ -80,10 +87,10 @@ However, for running more complicated versions of the workflow, additional input
 
 * **sampleids** - sample ids for provided gVCF files. Can be inferred if not provided.
 * **chrs** - chromsones to run on.
-* **refsdir** -
-* **mapsdir** -
-* **panelnocallbed** - 
-* **panelcallbed** - 
+* **refsdir**
+* **mapsdir**
+* **panelnocallbed**
+* **panelcallbed**
 
 Some boolean parameters are used for the conditional execution of the main workflow.