diff options
| -rw-r--r-- | ccwl/ccwl.scm | 87 |
1 files changed, 47 insertions, 40 deletions
diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm index a9745b1..b1425f8 100644 --- a/ccwl/ccwl.scm +++ b/ccwl/ccwl.scm @@ -61,7 +61,6 @@ (cons 'default (input-default input))))) ,@(input-other input))) -(define* (workflow steps outputs #:key (other '())) (define-immutable-record-type <step> (make-step id run in out) step? @@ -111,47 +110,55 @@ (string=? (input-id input1) (input-id input2))) +(define* (workflow id steps outputs #:key (other '())) "Build a Workflow class CWL workflow." - `((cwlVersion . "v1.1") - (class . Workflow) - ,@other - (inputs . ,(delete-duplicates - (map input->tree - (append - (append-map (lambda (step) - (filter-map (match-lambda - ((id . (? input? input)) input) - ((? input? input) input) - (_ #f)) + (let* ((inputs + ;; When the same input is used by multiple steps, there will + ;; be duplicates. So, deduplicate. + (delete-duplicates + (append (append-map step-in steps) + ;; If an input is directly copied to the output, an + ;; output-source will be an <input> object. + (filter-map (lambda (output) + (and (input? (output-source output)) + (output-source output))) + outputs)) + input=?)) + ;; List of non-internal inputs that should be interfaced with + ;; the outside world. + (interface-inputs + (filter (lambda (input) + (string=? (input-id input) + (input-source input))) + inputs))) + (make-step id + `((cwlVersion . "v1.1") + (class . Workflow) + (requirements (Subworkflow-feature-requirement)) + ,@other + (inputs . ,(map input->tree interface-inputs)) + (outputs . ,(map (lambda (output) + `(,(output-id output) + (type . ,(output-type output)) + (output-source . ,(match (output-source output) + ((? string? source) source) + ((? input? input) (input-id input)))))) + outputs)) + (steps . ,(map (lambda (step) + `(,(step-id step) + (in . ,(map (lambda (input) + (cons (input-id input) + (input-source input))) (step-in step))) - steps) - (filter-map (lambda (output) - (and (input? (workflow-output-source output)) - (workflow-output-source output))) - outputs))))) - (outputs . ,(map (lambda (output) - `(,(workflow-output-id output) - (type . ,(workflow-output-type output)) - (output-source . ,(match (workflow-output-source output) - ((? string? source) source) - ((? input? input) (input-id input)))))) - outputs)) - (steps . ,(map (lambda (step) - `(,(step-id step) - (in . ,(map (match-lambda - ((id . input) - (cons id (if (input? input) - (input-id input) - input))) - ((? input? input) - (cons (input-id input) (input-id input))) - ((? intermediate? intermediate) - (cons (input-id (intermediate-input intermediate)) - (intermediate-output-source intermediate)))) - (step-in step))) - (out . ,(list->vector (step-out step))) - (run . ,(step-run step)))) - steps)))) + (out . ,(list->vector (map output-id (step-out step)))) + (run . ,(match (step-run step) + ((? command? command) + (command->cwl command)) + (tree tree))))) + steps))) + interface-inputs + outputs))) + (define (output->cwl output) `(,(output-id output) ,@(filter identity |