ccwl: Support staging input files.

* ccwl/ccwl.scm (<input>)[stage?]: New field.
* ccwl/ccwl.scm (input): Add #:stage argument.
* ccwl/cwl.scm (command->cwl-scm): Serialize requirements for staged
inputs.
* doc/ccwl.skb (Cookbook)[Stage input files]: New section.
* tests/ccwl.scm ("inputs with an invalid #:stage? parameter must
raise a &ccwl-violation condition"): New test.

1 files changed, 9 insertions, 0 deletions

diff --git a/doc/ccwl.skb b/doc/ccwl.skb
index 39116ee..69e5a38 100644
--- a/doc/ccwl.skb
+++ b/doc/ccwl.skb
@@ -323,6 +323,15 @@ misspelt words appear at the output.]
          (prog :line #f (source :file "doc/spell-check.out")))))
 
   (chapter :title [Cookbook]
+    (section :title [Stage input files]
+      (p [When running command-line tools, CWL normally has separate
+directories for input and output files. But, some command-line tools
+expect their input and output files to be in the same directory, and
+this may not sit well with them. In such situations, we can tell CWL
+to ,(emph "stage") the input file into the output directory. We may
+express this in ccwl using the ,(code "#:stage?") parameter to the
+inputs to be staged. Here is a rather concocted example.]
+         (scheme-source "doc/staging-input-files.scm")))
     (section :title [Reuse external CWL workflows]
       (p [Even though you may be a ccwl convert (hurrah!), others may
 not be. And, you might have to work with CWL workflows written by