Various fixes, updated debug.md to use new format

config.yaml

@@ -42,7 +42,7 @@ episodes:
   - 02-shell_to_cwl.Rmd
   - 03-dependency_graphs.Rmd
   - 04-reusing_tools.Rmd
-  - debug.md
+  - addendum-01-debug.Rmd
   - more_info.md
 
 # Information for Learners

episodes/02-shell_to_cwl.Rmd

@@ -151,13 +151,16 @@ However, CWL syntax requires only that each field is properly defined, it does n
 
 :::::::::::::::::::::::::::::::::::::: challenge
 
+### Changing the output string 🌶
+
 What do you need to change to print a different text on the command line?
 
 :::::::::::::::::::::::::::::::::::::::::::::
 
 
 :::::::::::::::::::::::::::::::::::::: solution
 
+
 To change the text on the command line, you only have to change the text in the `hello_world.yml` file.
 
 For example
@@ -170,6 +173,8 @@ message_text: Good job!
 
 :::::::::::::::::::::::::::::::::::::: challenge
 
+### Updating the arguments 🌶🌶
+
 How can one add the `-e` argument to the echo command to interpret backslashes?
 
 :::::::::::::::::::::::::::::::::::::::::::::
@@ -188,6 +193,8 @@ arguments:
 
 :::::::::::::::::::::::::::: challenge
 
+### Redirecting cwltool stdout and stderr 🌶🌶
+
 Rerun the `echo.cwl` script but point stdout and stderr to different files.
 
 What is the difference between the stdout and stderr from the `echo.cwl` script?
@@ -196,7 +203,7 @@ What is the difference between the stdout and stderr from the `echo.cwl` script?
 
 :::::::::::::::::::::::::::: hint
 
-### Hint: Redirecting stdout and stderr
+### Hint: Redirecting CLI stdout and stderr
 
 Use the redirectors `1>` and `2>` to redirect stdout and stderr to different files respectively
 
@@ -212,7 +219,7 @@ $ cwltool echo.cwl hello_world.yml 1>echo_stdout.txt 2>echo_stderr.txt
 
 :::::::::::::::::::::::::::: challenge
 
-### Specifying the outputs of the tool as an actual output
+### Specifying the stdout of the tool as a CWL output 🌶🌶🌶
 
 Using [this tutorial][capturing_stdout_tutorial] as a guide
 
@@ -228,7 +235,7 @@ How does this change the output of the cwltool command?
 
 :::::::::::::::::::::::::::: hint
 
-### OutputBinding
+### Hint - stdout output binding
 
 Copy the 'outputBinding' from the tutorial 'verbatim'.
 
@@ -458,6 +465,8 @@ delete the `cache` directory anytime, if you need to reclaim the disk space.
 
 :::::::::::::::::::::::::::::::::::::: challenge
 
+### Directly embed a Commandlinetool into a file 🌶🌶
+
 How could one embed the fastqc tool description directly into the workflow?
 
 ::::::::::::::::::::::::::::::::::::::
@@ -487,7 +496,7 @@ steps:
 
 ::::::::::::::::::::::::::::::::::::::
 
-:::::::::::::::::::::::::::::::::::::: discussion
+:::::::::::::::::::::::::::::::::::::: callout
 
 ### Embedding Tool Descriptions
 

episodes/03-dependency_graphs.Rmd

@@ -5,19 +5,23 @@ exercises: 0
 ---
 
 ::::::::::::::::::::::::::::: questions
+
 - How can we expand to a multi-step workflow?
 - Iterative workflow development
 - Workflows as dependency graphs
 - How to use sketches for workflow design?
+
 :::::::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::: objectives
+
 - Explain that a workflow is a dependency graph
 - Use cwlviewer online
 - Generate Graphviz diagram using cwltool
 - Exercise with the printout of a simple workflow; draw arrows on code; hand draw a graph on another sheet of paper
 - Recognise that workflow development can be iterative i.e. that it doesn't have to happen all at once
 - Understand the flow of data between tools
+
 :::::::::::::::::::::::::::::
 
 
@@ -82,7 +86,6 @@ the `mapping_reads` step definition with a `ResourceRequirement` to allocate a m
 :::::::::::::::::::::::
 
 
-
 The newly added `mapping_reads` step also need an input not provided by any of our other steps,
 therefore an additional workflow-level input is added: a directory that contains the reference genome
 necessary for the mapping.
@@ -102,7 +105,7 @@ This `ref_fruitfly_genome` is added in the `inputs` field of the workflow and in
 
 ::::::::::::::::::::::::::::: challenge
 
-### Exercise: Draw the workflow
+### Challenge: Draw the workflow 🌶
 
 Draw the connecting arrows in the following graph of our workflow. Also, provide the outputs/inputs
 of the different steps. You can use for example Paint or print out the graph.

episodes/04-reusing_tools.Rmd

@@ -29,7 +29,7 @@ The last step of our workflow is counting the RNA-seq reads for which we will us
 
 :::::::::::::::::::::::::::::: challenge
 
-### Find the featureCounts tool in the bio-cwl-tools library
+### Find the featureCounts tool in the bio-cwl-tools library 🌶
 
 Find the `featureCounts` tool in the [bio-cwl-tools library][bio-cwl-tools].
 Have a look at the CWL document. Which inputs does this tool need? And what are the outputs of this tool?
@@ -39,6 +39,7 @@ Have a look at the CWL document. Which inputs does this tool need? And what are
 :::::::::::::::::::::::::::::: solution
 
 The `featureCounts` CWL document can be found in the [GitHub repo][featurecounts-cwl].
+
 It has three inputs:
 - annotations
   - A GTF or GFF file containing the gene annotations
@@ -62,13 +63,13 @@ so the tool should be located at `bio-cwl-tools/subread/featureCounts.cwl`.
 
 ::::::::::::::::::::::::::::: challenge
 
-### Add the featureCounts tool to the workflow
+### Add the featureCounts tool to the workflow 🌶🌶
 
 Please copy the `rna_seq_workflow_2.cwl` file to create `rna_seq_workflow_3.cwl`.
 
 Add the `featureCounts` tool to the workflow as a workflow step.
 
-**Bonus**: 
+**Bonus**: 🌶🌶🌶
 
 Similar to the `STAR` tool, this tool also needs more RAM than the default.