Update links to references

Renamed workflow to 'workflow definition' when referring to the cwl file but also referencing running the workflow and the workflow inputs.

episodes/01-introduction.Rmd

@@ -110,8 +110,8 @@ The rise in popularity of workflows has been matched by a rise in the
 number of disparate workflow managers that are available, each with their own 
 syntax or methods for describing the tools and workflows, reducing portability 
 and interoperability of these workflows. For a comprehensive lists of all known 
-computational workflow systems, see [Computational Data Analysis Workflow Systems](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems)
-maintained by the CWL community. The Common Workflow Language [CWL](https://www.commonwl.org) 
+computational workflow systems, see [Computational Data Analysis Workflow Systems][computational_data_analysis_workflow_systems]
+maintained by the CWL community. The Common Workflow Language [CWL][cwl_home] 
 standard has been developed to address these problems, and to serve as a
 open standard for describing how to run commandline tools and connect them
 to create workflows.
@@ -198,5 +198,8 @@ workflow will be set up to connect these tools and generate the desired output f
 [^3]: M. Wilkinson, M. Dumontier, I. Aalbersberg, et al. (2016): The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. [https://doi.org/10.1038/sdata.2016.18](https://doi.org/10.1038/sdata.2016.18)
 [^4]: 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](https://doi.org/10.1145/3486897)
 
+[cwl_home]: https://www.commonwl.org
+[computational_data_analysis_workflow_systems]: https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems
 [docker]: https://www.docker.com/
 [yaml_guide]: https://www.commonwl.org/user_guide/topics/yaml-guide.html
+

episodes/03-dependency_graphs.Rmd

@@ -28,10 +28,10 @@ exercises: 0
 ## Multi-Step Workflow
 
 In the previous episode we worked through a single step workflow, carrying out quality control check
-on RNA read of the fruitfly genome. In this episode the workflow is extended with an equivalent reverse
-RNA read and the next two steps of the RNA-sequencing analysis, trimming the reads and
+on RNA reads of the fruitfly genome. In this episode the workflow is extended with an equivalent reverse
+RNA reads and the next two steps of the RNA-sequencing analysis, trimming the reads and
 aligning the trimmed reads, are added.
-We will be using the [`cutadapt`](https://bio.tools/cutadapt)  and [`STAR`](https://bio.tools/star) tools for these tasks.
+We will be using the [`cutadapt`][cutadapt]  and [`STAR`][star] tools for these tasks.
 
 To make a multi-step workflow that can carry all this analysis out, we add more entries
 to the `steps` field. 
@@ -95,7 +95,7 @@ This `ref_fruitfly_genome` is added in the `inputs` field of the workflow and in
 
 ## Running the new workflow
 
-The workflow is complete and we only need to complete the YAML input file.
+The workflow definition is complete and we now only need to write the YAML input file.
 
 ::::::::::::::::::::::: spoiler
 
@@ -107,7 +107,7 @@ The workflow is complete and we only need to complete the YAML input file.
 
 :::::::::::::::::::::::
 
-You have finished the workflow and the input file and now you can run the whole workflow.
+We  have finished the workflow definition and the input file and now can run the workflow.
 
 ```bash
 cwltool --cachedir cache rna_seq_workflow_2.cwl workflow_input_2.yml
@@ -127,8 +127,9 @@ of the different steps. You can use for example Paint or print out the graph.
 :::::::::::::::::::::::::::: solution
 
 ### Solution
- To find out how the inputs and the steps are connected to each other, you look at the `in` field
- of the different steps.
+
+To find out how the inputs and the steps are connected to each other, look at the `in` field
+of the different steps.
 
 ![](fig/Ep3_graph_answer.png){alt="Ep3 empty graph answer" style='height: "300px"'}
 
@@ -137,6 +138,7 @@ of the different steps. You can use for example Paint or print out the graph.
 :::::::::::::::::::::::::::: callout
 
 ## Iterative working
+
 Working on a workflow is often not something that happens all at once.
 Sometimes you already have a shell script ready that can be converted to a CWL workflow.
 Other times it is similar to this tutorial, you start with a single-step workflow and extend it to
@@ -174,8 +176,8 @@ workflow-level input or the presence of a particular output from another step.
 ### From CWL script to graph
 
 In this example the workflow is already made, so the graph can be generated using
-[cwlviewer](https://view.commonwl.org/) online or using `cwltool`. First, let's have a look at
-[cwlviewer](https://view.commonwl.org/). To use this tool, the workflow has to be put in a GitHub,
+[cwlviewer][cwl_viewer] online or using `cwltool`. First, let's have a look at
+[cwlviewer][cwl_viewer]. To use this tool, the workflow has to be put in a GitHub,
 GitLab or Git repository. To view the graph of the workflow enter the URL and click `Parse Workflow`.
 
 The cwlviewer displays the workflow as a graph, starting with the input. Then the different steps
@@ -195,7 +197,7 @@ cwltool --print-dot rna_seq_workflow_2.cwl | dot -Tsvg > workflow_graph_2.svg
 ```
 
 The resulting SVG file displays the same graph as the one in the cwlviewer. The SVG file can be
-opened in any web browser and in [Inkscape](https://inkscape.org/), for example.
+opened in any web browser and in [Inkscape][inkscape], for example.
 
 :::::::::::::::::::::::::::::::: callout
 
@@ -207,7 +209,7 @@ Windows users can run `wslview workflow_graph_2.svg` in their terminal to view t
 
 ### Visualisation in VSCode
 
-[__Benten__](https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl) is an extension
+[__Benten__][benten] is an extension
 in Visual Studio Code (VSCode) that among other things visualises a workflow in a graph. When Benten
 is installed in VSCode, the tool can be used to visualise the workflow. In the top-right corner of
 the VSCode window the CWL viewer can be opened, see the screenshot below.
@@ -230,3 +232,8 @@ The graph by VSCode/Benten doesn't show the output-input names between the diffe
 
 ::::::::::::::::::::::::
 
+[cwl_viewer]: https://view.commonwl.org/
+[inkscape]: https://inkscape.org/
+[benten]: https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl
+[cutadapt]: https://bio.tools/cutadapt
+[star]: https://bio.tools/star

episodes/04-reusing_tools.Rmd

@@ -25,7 +25,7 @@ The CWL documents of the previous steps were already provided for you, however,
 In this episode you will use the bio-cwl-tools library to add the last step to the workflow.
 
 ## Adding new step in workflow
-The last step of our workflow is counting the RNA-seq reads for which we will use the [`featureCounts`](https://bio.tools/featurecounts) tool.
+The last step of our workflow is counting the RNA-seq reads for which we will use the [`featureCounts`][featurecounts] tool.
 
 :::::::::::::::::::::::::::::: challenge
 
@@ -135,10 +135,11 @@ cwltool --cachedir cache rna_seq_workflow_3.cwl workflow_input_3.yml
 
 ::::::::::::::::::::::::::::: keypoints
 
-- [bio-cwl-tools](https://github.com/common-workflow-library/bio-cwl-tools) is a library of CWL documents for biology/life-sciences related tools
+- [bio-cwl-tools][bio-cwl-tools] is a library of CWL documents for biology/life-sciences related tools
 
 :::::::::::::::::::::::::::
 
 
 [bio-cwl-tools]: https://github.com/common-workflow-library/bio-cwl-tools
+[featurecounts]: https://bio.tools/featurecounts
 [featurecounts-cwl]: https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl