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authorArun Isaac2021-05-23 14:45:25 +0530
committerArun Isaac2021-05-24 16:25:44 +0530
commit9d6aa0915d210efe3f92bbf3058425733ceacb7b (patch)
treed08a790676e5c89798be1ad16c1e6d488076a5b0
parent16befac5d26e488a863202408433f42b8319c368 (diff)
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Add "Capturing stdout" section to tutorial.
* doc/ccwl.texi (Capturing the standard output stream of a command): New section. * doc/ccwl.texi (Tutorial): Link to "Capturing stdout" node from menu.
-rw-r--r--doc/ccwl.texi49
1 files changed, 49 insertions, 0 deletions
diff --git a/doc/ccwl.texi b/doc/ccwl.texi
index c61587f..f8a1e97 100644
--- a/doc/ccwl.texi
+++ b/doc/ccwl.texi
@@ -54,6 +54,7 @@ Guide}.
@menu
* 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
@end menu
@node Important concepts
@@ -156,6 +157,54 @@ Hello World!
Final process status is success
@end example
+@node Capturing stdout
+@section Capturing the standard output stream of a command
+
+Let us return to the ``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 as earlier with
+only the addition of an @code{stdout} type output object to the command
+definition.
+
+@lisp
+(define print
+ (command #:run "echo" (input 'message #:type 'string)
+ #:outputs (output 'printed-message #:type 'stdout)))
+
+(workflow ((message #:type string))
+ (print #:message message))
+@end lisp
+
+Let's write this code to a file @file{capture-stdout.scm}, generate CWL,
+write the generated CWL to @file{capture-stdout.cwl}, and run it using
+@code{cwltool}. We might expect something like the output below. Notice
+how the standard output of the @code{print} command has been captured in
+the file @file{51fe79d15e7790a9ded795304220d7a44aa84b48}.
+
+@example
+$ ccwl compile capture-stdout.scm > capture-stdout.cwl
+$ cwltool capture-stdout.cwl --message "Hello World!"
+[workflow ] start
+[workflow ] starting step print
+[step print] start
+[job print] /tmp/7zksx3xm$ echo \
+ 'Hello World!' > /tmp/7zksx3xm/51fe79d15e7790a9ded795304220d7a44aa84b48
+[job print] completed success
+[step print] completed success
+[workflow ] completed success
+@{
+ "printed-message": @{
+ "location": "file:///home/manimekalai/51fe79d15e7790a9ded795304220d7a44aa84b48",
+ "basename": "51fe79d15e7790a9ded795304220d7a44aa84b48",
+ "class": "File",
+ "checksum": "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b",
+ "size": 13,
+ "path": "/home/manimekalai/51fe79d15e7790a9ded795304220d7a44aa84b48"
+ @}
+@}
+Final process status is success
+@end example
+
@node Contributing
@chapter Contributing