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diff --git a/doc/ccwl.skb b/doc/ccwl.skb index 1ae35f2..bc15c21 100644 --- a/doc/ccwl.skb +++ b/doc/ccwl.skb @@ -22,6 +22,7 @@ (document :title [Concise Common Workflow Language] (toc) (chapter :title [Introduction] + :ident "chapter-introduction" (p [,(abbr :short "CWL" :long "Common Workflow Language") is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety @@ -36,12 +37,14 @@ from concise descriptions in ccwl. In the future, ccwl will also have a runtime whereby users can interactively execute workflows while developing them.])) (chapter :title [Tutorial] + :ident "chapter-tutorial" (p [This tutorial will introduce you to writing workflows in ccwl. Some knowledge of CWL is assumed. To learn about CWL, please see the ,(ref :url "https://www.commonwl.org/user_guide/" :text "Common Workflow Language User Guide")]) (section :title [Important concepts] + :ident "section-important-concepts" (p [The CWL and ccwl workflow languages are statically typed programming languages where functions accept multiple named inputs and return multiple named outputs. Let 's break @@ -71,6 +74,7 @@ function can return multiple output values as well. These multiple outputs are unordered and are each addressed by a unique name.]))) (section :title [First example] + :ident "section-first-example" (p [As is tradition, let us start with a simple ,(emph "Hello World") workflow in ccwl. This workflow accepts a string input and prints that string.]) @@ -113,6 +117,7 @@ as follows. The expected output is also shown.]) (prog :line #f (source :file "doc/hello-world.out"))) (section :title [Capturing the standard output stream of a command] + :ident "section-capturing-stdout" (p [Let us return to the ,(emph "Hello World") example in the previous section. But now, let us capture the standard output of the ,(code "print") command in an output object. The ccwl code is the same @@ -132,6 +137,7 @@ output of the ,(code "print") command has been captured in the file (prog :line #f (source :file "doc/capture-stdout.out"))) (section :title [Capturing output files] + :ident "section-capturing-output-files" (p [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.]) @@ -172,6 +178,7 @@ output.]) (prog :line #f (source :file "doc/capture-output-file-with-parameter-reference.out"))) (section :title [Passing input into the standard input stream of a command] + :ident "section-passing-input-into-stdin" (p [Some commands read input from their standard input stream. Let us do that from ccwl. The workflow below reports the size of a file by passing it into the standard input of @@ -187,6 +194,7 @@ input of ,(command "wc"), and the file size reported in bytes.]) (prog :line #f (source :file "doc/pass-stdin.out"))) (section :title [Workflow with multiple steps] + :ident "section-workflow-with-multiple-steps" (p [Till now, we have only written trivial workflows with a single command. If we were only interested in executing single commands, we would hardly need a workflow language! So, in this @@ -249,6 +257,7 @@ following output.]) "md5"), ,(file "sha1") and ,(file "sha256") respectively.]))) (section :title [Let's write a spell check workflow] + :ident "section-spell-check-workflow" (p [Finally, let's put together a complex workflow to understand how everything fits together. The workflow we will be attempting is a spell check workflow inspired by the founders of Unix,(footnote @@ -323,7 +332,9 @@ misspelt words appear at the output.] (prog :line #f (source :file "doc/spell-check.out"))))) (chapter :title [Cookbook] + :ident "chapter-cookbook" (section :title [Stage input files] + :ident "section-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 @@ -333,11 +344,13 @@ 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 [Array types] + :ident "section-array-types" (p [ccwl supports array types using the following syntax.] (scheme-source "doc/array-types.scm")) (p [Nested array types are also supported.] (scheme-source "doc/nested-array-types.scm"))) (section :title [Scatter/gather] + :ident "section-scatter-gather" (p [ccwl supports CWL's dotproduct scatter/gather feature using the following syntax. Here, the ,(code [other-messages]) input to the workflow is an array of strings that is scattered over the ,(code @@ -345,6 +358,7 @@ workflow is an array of strings that is scattered over the ,(code ,(code [other-messages]) as its ,(code [other-message]) argument.] (scheme-source "doc/scatter-gather.scm"))) (section :title [Reuse external CWL workflows] + :ident "section-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 others. ccwl permits easy reuse of external CWL workflows, and free @@ -360,6 +374,7 @@ the external CWL workflow.] (prog :line #f (source :file "doc/echo.cwl"))))) (chapter :title [Contributing] + :ident "chapter-contributing" (p [ccwl is developed on GitHub at ,(ref :url "https://github.com/arunisaac/ccwl"). Feedback, suggestions, feature requests, bug reports and pull requests are all |