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.

4 files changed, 46 insertions, 5 deletions

diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm
index fc6a152..98bc8ae 100644
--- a/ccwl/ccwl.scm
+++ b/ccwl/ccwl.scm
@@ -64,6 +64,7 @@
             input-default
             input-position
             input-prefix
+            input-stage?
             input-other
             output?
             output-id
@@ -79,7 +80,7 @@
             unspecified-default?))
 
 (define-immutable-record-type <input>
-  (make-input id type label default position prefix other)
+  (make-input id type label default position prefix stage? other)
   input?
   (id input-id)
   (type input-type)
@@ -87,6 +88,7 @@
   (default input-default set-input-default)
   (position input-position set-input-position)
   (prefix input-prefix set-input-prefix)
+  (stage? input-stage?)
   (other input-other))
 
 (define-immutable-record-type <unspecified-default>
@@ -127,14 +129,20 @@
                  (()
                   (condition (ccwl-violation input-spec)
                              (formatted-message "Input has no identifier")))))))
-       (apply (syntax-lambda** (id #:key (type #'File) label (default (make-unspecified-default)) (other #''()))
+       (apply (syntax-lambda** (id #:key (type #'File) label (default (make-unspecified-default)) (stage? #'#f) (other #''()))
+                (unless (memq (syntax->datum stage?)
+                              (list #t #f))
+                  (raise-exception
+                   (condition (ccwl-violation stage?)
+                              (formatted-message "Invalid #:stage? parameter ~a. #:stage? must either be #t or #f."
+                                                 (syntax->datum stage?)))))
                 (let ((position #f)
                       (prefix #f))
                   #`(make-input '#,id '#,type #,label
                                 #,(if (unspecified-default? default)
                                       #'(make-unspecified-default)
                                       default)
-                                #,position #,prefix #,other)))
+                                #,position #,prefix #,stage? #,other)))
               #'(id args ...))))
     (id (identifier? #'id) (input #'(id)))
     (_ (error "Invalid input:" (syntax->datum input-spec)))))
@@ -413,7 +421,7 @@ identifiers defined in the commands."
     (make-cwl-workflow file
                        (map (match-lambda
                               ((id . type)
-                               (make-input id type #f #f #f #f #f)))
+                               (make-input id type #f #f #f #f #f #f)))
                             (parameters->id+type (assoc-ref yaml "inputs")))
                        (map (match-lambda
                               ((id . type)
diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm
index 6c28175..f5d7f6a 100644
--- a/ccwl/cwl.scm
+++ b/ccwl/cwl.scm
@@ -24,6 +24,7 @@
 ;;; Code:
 
 (define-module (ccwl cwl)
+  #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
   #:use-module (ccwl ccwl)
   #:use-module (ccwl utils)
@@ -120,7 +121,19 @@ CWL YAML specification."
   "Render COMMAND, a <command> object, into a CWL tree."
   `((cwlVersion . ,%cwl-version)
     (class . CommandLineTool)
-    (requirements . ,(command-requirements command))
+    (requirements
+     ,@(if (any input-stage? (command-inputs command))
+           ;; Stage any inputs that need to be.
+           `((InitialWorkDirRequirement
+              (listing . ,(list->vector
+                           (filter-map (lambda (input)
+                                         (and (input-stage? input)
+                                              (string-append "$(inputs."
+                                                             (symbol->string (input-id input))
+                                                             ")")))
+                                       (command-inputs command))))))
+           '())
+     ,@(command-requirements command))
     ,@(command-other command)
     (arguments . ,(list->vector
                    ;; Put string arguments into the arguments array.
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
diff --git a/tests/ccwl.scm b/tests/ccwl.scm
index b26e854..e60a035 100644
--- a/tests/ccwl.scm
+++ b/tests/ccwl.scm
@@ -274,4 +274,15 @@
                       #:run "echo" (-x number)))
            #f)))
 
+(test-assert "inputs with an invalid #:stage? parameter must raise a &ccwl-violation condition"
+  (guard (exception
+          (else (and (ccwl-violation? exception)
+                     (string=? (formatted-message-format exception)
+                               "Invalid #:stage? parameter ~a. #:stage? must either be #t or #f."))))
+    (begin (macroexpand
+            '(command #:inputs (file #:type File
+                                     #:stage? 42)
+                      #:run "cat" file))
+           #f)))
+
 (test-end "ccwl")