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diff --git a/doc/ccwl.texi b/doc/ccwl.texi index 6e1a96d..c61587f 100644 --- a/doc/ccwl.texi +++ b/doc/ccwl.texi @@ -53,6 +53,7 @@ Guide}. @menu * Important concepts:: Static typing, multiple named inputs and outputs +* First example:: Our first ccwl workflow @end menu @node Important concepts @@ -96,6 +97,65 @@ return a single output value. However, in CWL, a function can return multiple output values as well. These multiple outputs are unordered and are each addressed by a unique name. +@node First example +@section First example + +As is tradition, let us start with a simple ``Hello World'' workflow in +ccwl. This workflow accepts a string input and prints that string. + +@lisp +(define print + (command #:run "echo" (input 'message #:type 'string))) + +(workflow ((message #:type string)) + (print #:message message)) +@end lisp + +The first form in this code defines the @code{print} command. This form +is the equivalent of defining a @code{CommandLineTool} class workflow in +CWL. All arguments after @code{#:run} specify the command that will be +run. One of those arguments @code{(input 'message #:type 'string)} +refers to a @code{string} type input named @code{message}. Notice how +the command definition is very close to a shell command, only that it is +slightly annotated with inputs and their types. + +The second form describes the actual workflow and is the equivalent of +defining a @code{Workflow} class workflow in CWL. The form +@code{((message #:type string))} specifies the inputs of the +workflow. In this case, there is only one input---@code{message} of type +@code{string}. The body of the workflow specifies the commands that will +be executed. The body of this workflow executes only a single +command---the @code{print} command---passing the @code{message} input of +the workflow as the @code{message} input to the @code{print} command. + +If this workflow is written to a file @file{hello-world.scm}, we may +compile it to CWL by running + +@example +$ ccwl compile hello-world.scm +@end example + +This prints a big chunk of generated CWL to standard output. We have +achieved quite a lot of concision already! We write the generated CWL to +a file and execute it using @code{cwltool} as follows. The expected +output is also shown. + +@example +$ ccwl compile hello-world.scm > hello-world.cwl +$ cwltool hello-world.cwl --message "Hello World!" +[workflow ] start +[workflow ] starting step echo +[step echo] start +[job echo] /tmp/zprgn3x0$ echo \ + 'Hello World!' +Hello World! +[job echo] completed success +[step echo] completed success +[workflow ] completed success +@{@} +Final process status is success +@end example + @node Contributing @chapter Contributing |