added staging files episode

Author: Toby Hodges

_episodes/15-staging.md

@@ -0,0 +1,48 @@
+---
+title: "Staging Input Files"
+teaching: 10
+exercises: 0
+questions:
+- "How do I stage input files in the working directory?"
+objectives:
+- "Learn how to handle situations where a tool expects to write output files to
+the same directory as its input files."
+keypoints:
+- "Input files are normally kept in a read-only directory."
+- "Use `InitialWorkDirRequirement` to stage input files in the working
+directory."
+---
+Normally, input files are located in a read-only directory separate from
+the output directory.  This causes problems if the underlying tool expects to
+write its output files alongside the input file in the same directory.  You use `InitialWorkDirRequirement` to stage input files into the output directory.
+In this example, we use a Javascript expression to extract the base name of the 
+input file from its leading directory path.
+
+*linkfile.cwl*
+
+```
+{% include cwl/linkfile.cwl %}
+```
+
+*arguments-job.yml*
+
+```
+{% include cwl/arguments-job.yml %}
+```
+
+Now invoke `cwl-runner` with the tool wrapper and the input object on the
+command line:
+
+```
+$ cwl-runner linkfile.cwl arguments-job.yml
+[job 139928309171664] /home/example$ docker run -i --volume=/home/example/Hello.java:/var/lib/cwl/job557617295_examples/Hello.java:ro --volume=/home/example:/var/spool/cwl:rw --volume=/tmp/tmpmNbApw:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1001 --rm --env=TMPDIR=/tmp java:7 javac Hello.java
+Final process status is success
+{
+"classfile": {
+  "size": 416,
+  "location": "/home/example/Hello.class",
+  "checksum": "sha1$2f7ac33c1f3aac3f1fec7b936b6562422c85b38a",
+  "class": "File"
+  }
+}
+```