From 2853ef38886e3ffd7f12252ab17fb2d4e29614e2 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Tue, 17 Oct 2023 19:16:50 +0100 Subject: ccwl: Support staging input files. * ccwl/ccwl.scm ()[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. --- doc/ccwl.skb | 9 +++++++++ 1 file changed, 9 insertions(+) (limited to 'doc') diff --git a/doc/ccwl.skb b/doc/ccwl.skb index 39116ee..69e5a38 100644 --- a/doc/ccwl.skb +++ b/doc/ccwl.skb @@ -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 -- cgit v1.2.3