ccwl: Factorize out CWL generation code to separate file.

This factorization is required to support other compilation targets
such as graphviz, bash, scheme, etc.

* ccwl/cwl.scm: New file.
* Makefile.am (SOURCES): Register it.
* ccwl/ccwl.scm (ccwl): Export command?, command-inputs,
command-outputs, command-args, command-stdin, command-other,
workflow?, workflow-steps, workflow-inputs, workflow-outputs,
workflow-other, input?, input-id, input-type, input-label,
input-default, input-position, input-prefix, input-other, output?,
output-id, output-type, output-binding, output-source, output-other,
step?, step-id, step-run, step-in, step-out, unspecified-default?.
(<workflow>): New type.
(filter-alist): Move to cwl.scm.
(make-workflow): Refactor into workflow->cwl-scm in cwl.scm.
(output->cwl): Move to cwl.scm as output->cwl-scm.
(command->cwl): Move to cwl.scm as command->cwl-scm.
(workflow-steps): Rename to collect-steps. Clarify docstring.
(workflow): Use collect-steps instead of workflow-steps. Explicitly
pass empty list as other argument of make-workflow. Add TODO note to
implement it properly.
* scripts/ccwl.in: Import (ccwl cwl) instead of (ccwl yaml). Use
workflow->cwl instead of scm->yaml.
* tests/ccwl.scm ("stdin input should not have inputBinding"): Use
command->cwl-scm from (ccwl cwl) instead of command->cwl from (ccwl
ccwl).

1 files changed, 2 insertions, 2 deletions

diff --git a/tests/ccwl.scm b/tests/ccwl.scm
index dfdc7c0..8cbe009 100644
--- a/tests/ccwl.scm
+++ b/tests/ccwl.scm
@@ -25,8 +25,8 @@
   (not (assoc-ref
         (assoc-ref
          (assoc-ref
-          ((module-ref (resolve-module '(ccwl ccwl))
-                       'command->cwl)
+          ((module-ref (resolve-module '(ccwl cwl))
+                       'command->cwl-scm)
            (command #:inputs (file #:type 'File)
                     #:run "wc" "-c"
                     #:stdin file))