Create README.md

test/README.md

@@ -0,0 +1,26 @@
+
+# SEAseq and PEAseq "sub-sampled" dataset example run.
+Please consult [documentation](https://github.com/stjude/seaseq/tree/master/docs#readme) for more details.
+
+## Prerequisites
+1. Docker (installed and running)
+2. Cromwell.jar (> 51)
+
+## Usage
+### 1. Local OS (NOT recommended for real datasets)
+``` sh
+# replace <cromwell.jar> with actual cromwell.jar version downloaded
+java -jar <cromwell.jar> run ../seaseq-case.wdl -i inputs-s_case.json -o options-s_case.json
+```
+
+### 2. HPC 
+
+``` bash
+# replace <hpc.config> with the applicable hpc configuration file
+# replace <cromwell.jar> with actual cromwell.jar version downloaded
+java -Dconfig.file=<hpc.config> -jar <cromwell.jar> run ../seaseq-case.wdl -i inputs-s_case.json -o options-s_case.json
+```
+View our provided list of [hpc configuration](https://github.com/stjude/seaseq/tree/master/docs/hpc-configurations) files.
+
+## Further Details
+Consult bash scripts (\*.sh) provided for more details of actual run.