From 49daffbe3d572679d800d1757c59bc5d321b9cb5 Mon Sep 17 00:00:00 2001 From: Gerard Capes Date: Thu, 20 Jan 2022 12:40:25 +0000 Subject: [PATCH] Add YAML prerequisite and link to YAML guide (#64) Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- _episodes/01-introduction.md | 3 ++- index.md | 3 +++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/_episodes/01-introduction.md b/_episodes/01-introduction.md index 4b75705..048f054 100644 --- a/_episodes/01-introduction.md +++ b/_episodes/01-introduction.md @@ -34,7 +34,7 @@ Although these scripts might provide a direct means of accessing the tools, writ Shell scripts are not easily portable, and so researchers can easily end up spending more time maintaining the scripts than carrying out their research. The aim of CWL is to reduce that barrier of usage of these tools to researchers. -CWL workflows are written in a subset of YAML, with a syntax that does not restrict the amount of detail provided for a tool or workflow. +CWL workflows are written in a subset of [YAML], with a syntax that does not restrict the amount of detail provided for a tool or workflow. The execution model is explicit, all required elements of a tool's runtime environment must be specified by the CWL tool-description author. On top of these basic requirements they can also add hints or requirements to the tool-description, helping to guide users (and workflow engines) on what resources are needed for a tool. @@ -63,3 +63,4 @@ The different tools necessary for this analysis are already available. In this t {% include links.md %} [^1]: M. R. Crusoe, S. Abeln, A. Iosup, P. Amstutz, J. Chilton, N. Tijanić, H. Ménager, S. Soiland-Reyes, B. Gavrilović, C. Goble, The CWL Community (2021): Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Communication of the ACM. https://doi.org/10.1145/3486897 +[YAML]: http://www.commonwl.org/user_guide/yaml/ \ No newline at end of file diff --git a/index.md b/index.md index 7c112aa..ea2681c 100644 --- a/index.md +++ b/index.md @@ -49,6 +49,8 @@ for the tutorial material > tasks on a remote machine (by `ssh` connection) > and in a cluster (high performance computing) environment. > +> CWL is based upon YAML. At any time, if you find yourself being confused by the YAML syntax, considering reviewing this guide on the [subset of YAML][yaml-for-cwl] used in CWL. +> > If you have previously written a workflow description, > in CWL or another langauge, > you may want to look instead at the [User Guide][cwl-user-guide]. @@ -129,4 +131,5 @@ After following one of these tutorials, learners will be able to: [swc]: https://software-carpentry.org/ [swc-shell]: https://swcarpentry.github.io/shell-novice/ +[yaml-for-cwl]: https://www.commonwl.org/user_guide/yaml/ {% include links.md %}