diff options
| -rw-r--r-- | ccwl/ccwl.scm | 16 | ||||
| -rw-r--r-- | ccwl/cwl.scm | 15 | ||||
| -rw-r--r-- | doc/ccwl.skb | 9 | ||||
| -rw-r--r-- | tests/ccwl.scm | 11 |
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") |