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authorArun Isaac2023-10-17 19:16:50 +0100
committerArun Isaac2023-10-17 19:16:50 +0100
commit2853ef38886e3ffd7f12252ab17fb2d4e29614e2 (patch)
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ccwl: Support staging input files.
* ccwl/ccwl.scm (<input>)[stage?]: New field. * ccwl/ccwl.scm (input): Add #:stage argument. * ccwl/cwl.scm (command->cwl-scm): Serialize requirements for staged inputs. * doc/ccwl.skb (Cookbook)[Stage input files]: New section. * tests/ccwl.scm ("inputs with an invalid #:stage? parameter must raise a &ccwl-violation condition"): New test.
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@@ -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