Merge pull request #8 from aofarrel/order-enforcement

Order enforcement via whiskertail

Author: aofarrel

README.md

@@ -3,14 +3,24 @@ Mouse-sized WDL tasks for your workflows. 🐁
 
 Please add your suggestions to the Issues tab and flag them as enhancement.
 
-## arraycheck_simple
+## task-level
+
+### arraycheck_simple
 For performing a check between an array of truth files and an array of test files. It is assumed that the filenames between the truth and test files match. All md5 mismatches are reported, unless `fastfail == true` in which case the pipeline will fail immediately.
 
-## arraycheck_rdata
+### arraycheck_rdata
 Similar to arraycheck_exact, but upon md5 mismatch, an Rscript is run to check for functional equivalence via `all.equal(testfile, truthfile, tolerance)`. It is assumed that both checked files are RData files. The user may set the tolerance value, which defaults to 1.0e-8.
 
-## enumouse
+### enumouse
 Type `enum` exists in CWL, but not WDL. This task very roughly mimics the `enum` type by checking if a string is within an allowed set of values.
 
-## metamouse
+### filechecker
+Checks if two files are equivalent, as opposed to arraycheck_* iterating through two arrays. Includes the same Rdata equivalence checker of arraycheck_rdata (disabled by default).
+
+## workflow-level
+
+### metamouse
 Checker/Debugger for Stuart tasks. The test files are derived from the [WDL translation](https://github.com/DataBiosphere/analysis_pipeline_WDL) of the [UWGAC TOPMed Pipeline](https://github.com/UW-GAC/analysis_pipeline).
+
+### whiskertail
+Template for enforcing order in a WDL workspace. This could be useful if you want a workflow to fail early, rather than waste time/money on other steps.

whiskertail.json

@@ -0,0 +1,3 @@
+{  
+  "whiskertail.bogus": "Some backends require an input JSON, so we have one that does nothing."
+}

whiskertail.wdl

@@ -0,0 +1,45 @@
+version 1.0
+
+task simpletask {
+    input {
+        String echome
+    }
+
+    command <<<
+        echo "${echome}"
+    >>>
+
+    output {
+        String out = "The next task may now begin!"
+    }
+}
+
+workflow whiskertail {
+	input {
+		String bogus = "This doesn't ever get used, but an input is required for some backends."
+	}
+
+    if(back_paws.out != "") {
+        call simpletask as tail {
+            input:
+                echome = "I run last!"
+        }
+    }
+
+    call simpletask as front_paws {
+        input:
+            echome = whisker.out
+    }
+
+    call simpletask as whisker {
+        input:
+            echome = "I run first!"
+    }
+
+    if(front_paws.out != "") {
+        call simpletask as back_paws {
+            input:
+                echome = "I am the penultimate task!"
+        }
+    }
+}