Merge branch 'shell-commands'

Author: Peter Amstutz

draft-3/cwl-avro.yml

@@ -1143,7 +1143,12 @@
 
         When a binding is part of the `CommandLineTool.arguments` field,
         the `valueFrom` field is required.
-
+    - name: shellQuote
+      type: ["null", boolean]
+      doc: |
+        If `ShellCommandRequirement` is in the requirements for the current command,
+        this controls whether the value is quoted on the command line (default is true).
+        Use `shellQuote: false` to inject metacharacters for operations such as pipes.
 
 - type: record
   name: CommandOutputBinding
@@ -2044,3 +2049,15 @@
         the expression engine.  The semantics of this field are defined by the
         underlying expression engine.  Intended for uses such as providing
         function definitions that will be called from CWL expressions.
+
+- type: record
+  name: ShellCommandRequirement
+  extends: "#ProcessRequirement"
+  doc: |
+    Modify the behavior of CommandLineTool to generate a single string
+    containing a shell command line.  Each item in the argument list must be
+    joined into a string separated by single spaces and quoted to prevent
+    intepretation by the shell, unless `CommandLineBinding` for that argument
+    contains `shellQuote: false`.  If `shellQuote: false` is specified, the
+    argument is joined into the command string without quoting, which allows
+    the use of shell metacharacters such as `|` for pipes.

draft-3/draft-3/shelltest.cwl

@@ -0,0 +1,24 @@
+class: CommandLineTool
+description: "Reverse each line using the `rev` command then sort."
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  - id: "#input"
+    type: File
+outputs:
+  - id: "#output"
+    type: File
+    outputBinding:
+      glob: output.txt
+
+baseCommand: []
+arguments:
+  - rev
+  - valueFrom:
+      engine: cwl:JsonPointer
+      script: /job/input
+  - valueFrom: " | "
+    shellQuote: false
+  - sort
+  - valueFrom: "> output.txt"
+    shellQuote: false