More documentation for SFS caching options

README.md

@@ -1528,6 +1528,7 @@ Cromwell's call cache is maintained in its database.  For best mileage with call
 
 > **Note:** If call caching is enabled, be careful not to change the contents of the output directory for any previously run job.  Doing so might cause cache hits in Cromwell to copy over modified data and Cromwell currently does not check that the contents of the output directory changed.
 
+## Configuring Call Caching
 To enable Call Caching, add the following to your Cromwell [configuration](#configuring-cromwell):
 
 ```
@@ -1538,13 +1539,45 @@ call-caching {
 
 When `call-caching.enabled=true` (default: `false`), Cromwell will be able to to copy results from previously run jobs (when appropriate).
 
+## Call Caching Workflow Options
 Cromwell also accepts two [workflow option](#workflow-options) related to call caching:
 
 * If call caching is enabled, but one wishes to run a workflow but not add any of the calls into the call cache when they finish, the `write_to_cache` option can be set to `false`.  This value defaults to `true`.
 * If call caching is enabled, but you don't want to check the cache for any `call` invocations, set the option `read_from_cache` to `false`.  This value also defaults to `true`
 
 > **Note:** If call caching is disabled, the to workflow options `read_from_cache` and `write_to_cache` will be ignored and the options will be treated as though they were 'false'.
 
+## Local Filesystem Options
+When running a job on the Config (Shared Filesystem) backend, Cromwell provides some additional options in the backend's config section:
+
+```
+      config {
+        ...
+        filesystems {
+          ...
+          local {
+            ...
+            caching {
+              # When copying a cached result, what type of file duplication should occur. Attempted in the order listed below:
+              duplication-strategy: [
+                "hard-link", "soft-link", "copy"
+              ]
+
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              hashing-strategy: "file"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              check-sibling-md5: false
+            }
+          }
+        }
+      }
+```
+
 # REST API
 
 The `server` subcommand on the executable JAR will start an HTTP server which can accept WDL files to run as well as check status and output of existing workflows.

core/src/main/resources/reference.conf

@@ -163,6 +163,7 @@ backend {
             ]
 
             caching {
+              # When copying a cached result, what type of file duplication should occur. Attempted in the order listed below:
               duplication-strategy: [
                 "hard-link", "soft-link", "copy"
               ]