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diff --git a/doc/ccwl.texi b/doc/ccwl.texi index f8a1e97..e0223db 100644 --- a/doc/ccwl.texi +++ b/doc/ccwl.texi @@ -55,6 +55,7 @@ Guide}. * Important concepts:: Static typing, multiple named inputs and outputs * First example:: Our first ccwl workflow * Capturing stdout:: Capturing the standard output stream of a command +* Capturing output files:: Capturing output files produced by a command @end menu @node Important concepts @@ -205,6 +206,117 @@ $ cwltool capture-stdout.cwl --message "Hello World!" Final process status is success @end example +@node Capturing output files +@section Capturing output files + +In the previous section, we captured the standard output stream of a +command. But, how do we capture any output files created by a command? +Let us see. + +Consider a tar archive @file{hello.tar} containing a file +@file{hello.txt}. + +@example +$ tar --list --file hello.tar +hello.txt +@end example + +Let us write a workflow to extract the file @file{hello.txt} from the +archive. Everything in the following workflow except the +@code{#:binding} parameter will already be familiar to you. The +@code{#:binding} parameter sets the @code{outputBinding} field in the +generated CWL. In the example below, we set the @code{glob} field to +look for a file named @file{hello.txt}. + +@lisp +(define extract + (command #:run "tar" "--extract" "--file" (input 'archive #:type 'File) + #:outputs (output 'extracted-file + #:type 'File + #:binding '((glob . "hello.txt"))))) + +(workflow ((archive #:type File)) + (extract #:archive archive)) +@end lisp + +Writing this workflow to @file{capture-output-file.scm}, compiling and +running it gives us the following output. Notice that the file +@file{hello.txt} has been captured and is now present in our current +working directory. + +@example +$ ccwl compile capture-output-file.scm > capture-output-file.cwl +$ cwltool capture-output-file.cwl --archive hello.tar +[workflow ] start +[workflow ] starting step extract +[step extract] start +[job extract] /tmp/nrolttex$ tar \ + --extract \ + --file \ + /tmp/z7pp7qwh/stg3ac272aa-3459-4f20-a033-86f53ba72caf/hello.tar +[job extract] completed success +[step extract] completed success +[workflow ] completed success +@{ + "extracted-file": @{ + "location": "file:///home/manimekalai/hello.txt", + "basename": "hello.txt", + "class": "File", + "checksum": "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b", + "size": 13, + "path": "/home/manimekalai/hello.txt" + @} +@} +Final process status is success +@end example + +The above workflow is not awfully flexible. The name of the file to +extract is hardcoded into the workflow. Let us modify the workflow to +accept the name of the file to extract. We introduce @code{extractfile}, +a @code{string} type input that is passed to @command{tar} and is +referenced in the @code{glob} field. + +@lisp +(define extract-specific-file + (command #:run "tar" "--extract" "--file" (input 'archive #:type 'File) + (input 'extractfile #:type 'string) + #:outputs (output 'extracted-file + #:type 'File + #:binding '((glob . "$(inputs.extractfile)"))))) + +(workflow ((archive #:type File) (extractfile #:type string)) + (extract-specific-file #:archive archive #:extractfile extractfile)) +@end lisp + +Compiling and running this workflow gives us the following output. + +@example +$ ccwl compile capture-output-file.scm > capture-output-file.cwl +$ cwltool capture-output-file.cwl --archive hello.tar --extractfile hello.txt +[workflow ] start +[workflow ] starting step extract-specific-file +[step extract-specific-file] start +[job extract-specific-file] /tmp/751nydd1$ tar \ + --extract \ + --file \ + /tmp/1zzw2n6m/stgc851e003-b5bd-437e-844b-311f6f66a7f1/hello.tar \ + hello.txt +[job extract-specific-file] completed success +[step extract-specific-file] completed success +[workflow ] completed success +@{ + "extracted-file": @{ + "location": "file:///home/manimekalai/hello.txt", + "basename": "hello.txt", + "class": "File", + "checksum": "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b", + "size": 13, + "path": "/home/manimekalai/hello.txt" + @} +@} +Final process status is success +@end example + @node Contributing @chapter Contributing |