Expand create file example to show how to inject expressions into bash scripts

_episodes/14-runtime.md

@@ -4,16 +4,20 @@ teaching: 10
 exercises: 0
 questions:
 - "How do I create required input files from input parameters at runtime?"
+- "How do I invoke a script rather than just a simple command line?"
+- "How do I make inputs available to my script?"
 objectives:
 - "Learn how to create files on the fly during runtime."
+- "Learn how to use expressions in bash scripts."
 keypoints:
 - "Use `InitialWorkDirRequirement` to specify input files that need to be
 created during tool runtime."
 ---
 Sometimes you need to create a file on the fly from input parameters,
 such as tools which expect to read their input configuration from a file
-rather than the command line parameters.  To do this, use
-`InitialWorkDirRequirement`.
+rather than the command line parameters, or need a small wrapper shell script.  
+
+To generate such files we can use the `InitialWorkDirRequirement`.
 
 *createfile.cwl*
 
@@ -22,6 +26,12 @@ rather than the command line parameters.  To do this, use
 ~~~
 {: .source}
 
+Any [expressions](../13-expressions/index.html) like `$(inputs.message)` are expanded by the CWL engine before creating the file; here inserting the value at the input `message`. 
+
+> **Tip:** The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` should be **_escaped** with `\`, for instance `\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine.
+
+To test the above CWL tool use this job to provide the input value `message`:
+
 *echo-job.yml*
 
 ~~~
@@ -34,22 +44,26 @@ command line:
 
 ~~~
 $ cwl-runner createfile.cwl echo-job.yml
-[job createfile.cwl] /home/example$ cat \
-    example.conf > /home/example/output.txt
+[job createfile.cwl] /private/tmp/docker_tmphrqxxcdl$ sh \
+    example.sh > /private/tmp/docker_tmphrqxxcdl/output.txt
+Could not collect memory usage, job ended before monitoring began.
 [job createfile.cwl] completed success
 {
     "example_out": {
         "location": "file:///home/example/output.txt",
         "basename": "output.txt",
         "class": "File",
-        "checksum": "sha1$5d3f955d1bb862ec618bc2f7ca4c5fa29fa39e89",
-        "size": 22,
+        "checksum": "sha1$9045abe4bd04dd8ccfe50c6ff61820b784b64aa7",
+        "size": 25,
         "path": "/home/example/output.txt"
     }
 }
 Final process status is success
 $ cat output.txt
-CONFIGVAR=Hello world!
+Message is: Hello world!
 ~~~
 {: .output}
+
+
+
 {% include links.md %}

_includes/cwl/14-runtime/createfile.cwl

@@ -1,15 +1,15 @@
-#!/usr/bin/env cwl-runner
-
 class: CommandLineTool
 cwlVersion: v1.0
-baseCommand: ["cat", "example.conf"]
+baseCommand: ["sh", "example.sh"]
 
 requirements:
   InitialWorkDirRequirement:
     listing:
-      - entryname: example.conf
-        entry: |
-          CONFIGVAR=$(inputs.message)
+      - entryname: example.sh
+        entry: |-
+          PREFIX='Message is:'
+          MSG="\${PREFIX} $(inputs.message)"
+          echo \${MSG}
 
 inputs:
   message: string

_includes/cwl/conformance-test.yml

@@ -158,10 +158,10 @@
   output:
     example_out:
       class: File
-      checksum: sha1$5509385b089c054ac9f9890dccef666eda7eb79d
+      checksum: sha1$9045abe4bd04dd8ccfe50c6ff61820b784b64aa7
       basename: output.txt
       location: Any
-      size: 23
+      size: 25
 
 # Section 15
 - doc: Test for section 15