diff options
| -rw-r--r-- | ccwl/ccwl.scm | 181 |
1 files changed, 89 insertions, 92 deletions
diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm index e173d9e..547cf23 100644 --- a/ccwl/ccwl.scm +++ b/ccwl/ccwl.scm @@ -28,6 +28,7 @@ #:use-module (srfi srfi-9 gnu) #:use-module (srfi srfi-26) #:use-module (ice-9 match) + #:use-module (ccwl utils) #:use-module (ccwl yaml) #:export (command workflow @@ -127,104 +128,68 @@ (define append-command-outputs (field-appender command-outputs set-command-outputs)) -(define* (command id arguments #:key (additional-inputs '()) (outputs '()) (other '())) - (make-step id - (make-command additional-inputs outputs arguments #f other) - ;; A command can use the same input multiple times. So, - ;; deduplicate. - (delete-duplicates - (append (filter input? arguments) - additional-inputs) - input=?) - outputs)) +(define* (command #:key run (additional-inputs '()) (outputs '()) stdin (other '())) + (make-command additional-inputs outputs run stdin other)) (define (input=? input1 input2) (string=? (input-id input1) (input-id input2))) -(define (auto-connect steps) - "Auto-connect STEPS by matching inputs to outputs using their unique -identifiers. If any inputs are already matched, they are not -re-matched." - (map (lambda (step) - (set-step-in step - (map (lambda (input) - ;; If input is already connected, return - ;; it unaltered. Else, try to connect it - ;; to a source. - (cond - ((input-source input) - input) - ;; Input that should be connected to - ;; some intermediate output - ((find (lambda (step) - (member (input-id input) - (map output-id (step-out step)))) - steps) - => (lambda (source-step) - (set-input-source input - (string-append (step-id source-step) - "/" (input-id input))))) - ;; Non-internal input that should be - ;; interfaced with the outside world - (else input))) - (step-in step)))) - steps)) - -(define* (workflow id steps outputs #:key (other '())) +(define (invoke-command step-id command . args) + (make-step step-id + command + (plist->alist args) + (command-outputs command))) + +(define* (make-workflow steps outputs #:key (other '())) "Build a Workflow class CWL workflow." - (let* ((steps (auto-connect steps)) - (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 (remove input-source inputs))) - (make-step id - `((cwl-version . ,%cwl-version) - (class . Workflow) - (requirements (Subworkflow-feature-requirement)) - ,@other - (inputs . ,(map (lambda (input) - `(,(input-id input) - ,@(filter-alist - `((type . ,(input-type input)) - (label . ,(input-label input)) - (default . ,(and (not (unspecified-default? (input-default input))) - (input-default input))))) - ,@(input-other input))) - 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) - (or (input-source input) - (input-id input)))) - (step-in step))) - (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))) + `((cwl-version . ,%cwl-version) + (class . Workflow) + (requirements (Subworkflow-feature-requirement)) + ,@other + (inputs . ,(map (lambda (input) + `(,(input-id input) + ,@(filter-alist + `((type . ,(input-type input)) + (label . ,(input-label input)) + (default . ,(and (not (unspecified-default? (input-default input))) + (input-default input))))) + ,@(input-other input))) + ;; When the same input is used by multiple steps, + ;; there will be duplicates. So, deduplicate. + (delete-duplicates + (append-map (lambda (step) + (filter-map (match-lambda + ((_ . (? input? input)) + input) + (_ #f)) + (step-in step))) + steps) + input=?))) + (outputs . ,(map (lambda (output) + `(,(output-id output) + (type . ,(match (output-type output) + ('stdout 'File) + (some-other-type some-other-type))) + (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 (in) + (match in + ((id . (? string? source)) + in) + ((id . (? input? input)) + (cons id (input-id input))))) + (step-in step))) + (out . ,(list->vector (map output-id (step-out step)))) + (run . ,(match (step-run step) + ((? command? command) + (command->cwl command)) + (tree tree))))) + steps)))) (define* (pipeline id steps #:optional @@ -351,3 +316,35 @@ re-matched." (command->cwl run) run)) <>))) + +(define (workflow-steps x) + (syntax-case x () + ((command (step-id) args ...) + (cons #`(invoke-command + step-id command + #,@(append-map (lambda (pair) + (syntax-case pair () + ((key . (_ (id) _ ...)) + (list #'key (string-append + (syntax->datum #'id) + "/" (symbol->string + (keyword->symbol + (syntax->datum #'key)))))) + ((key . atom) + (list #'key #'atom)))) + (pairify #'(args ...)))) + (append-map workflow-steps #'(args ...)))) + (atom (list)))) + +(define-syntax workflow + (lambda (x) + (syntax-case x () + ((_ root) + #`(make-workflow + (list #,@(workflow-steps #'root)) + #,(syntax-case x () + ((_ (command (step-id) _ ...)) + #'(map (lambda (output) + (set-output-source + output (string-append step-id "/" (output-id output)))) + (command-outputs command))))))))) |