Update user settings json to have param tag

* Update yaml guide link as a footnote.
* Add callout for m1 users wrt libarchive

episodes/01-introduction.Rmd

@@ -138,7 +138,7 @@ 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](https://www.commonwl.org/user_guide/topics/yaml-guide.html), with a syntax that does not restrict the
+CWL workflows are written in a subset of [YAML][yaml_guide], 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.
@@ -199,3 +199,4 @@ workflow will be set up to connect these tools and generate the desired output f
 [^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)
 
 [docker]: https://www.docker.com/
+[yaml_guide]: https://www.commonwl.org/user_guide/topics/yaml-guide.html

learners/files/linux_setup.Rmd

@@ -112,7 +112,7 @@ For other Linux systems, check [the graphviz download page][graphviz_download_pa
 [vs_code]: https://code.visualstudio.com/
 [benten_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl
 [redhat_yaml_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml
-[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings
+[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings#_settingsjson
 [docker_server_install]: https://docs.docker.com/engine/install/#server
 [enable_user_docker_usage]: https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user
 [graphviz_download_page]: https://graphviz.org/download/#linux

learners/files/macos_setup.Rmd

@@ -24,7 +24,7 @@ Download and install [VSCode][vs_code]
 
 #### Attribute CWL files to the yaml file type
 
-Add the following chunk to the VSCode [user settings json][user_settings_json] in [settings.json](https://code.visualstudio.com/docs/getstarted/settings#_settingsjson) to attribute CWL to the YAML file type.
+Add the following chunk to the VSCode [user settings json][user_settings_json] to attribute CWL to the YAML file type.
 
 ```json
 {
@@ -60,6 +60,20 @@ conda config --add channels conda-forge
 
 <br>
 
+::::::::::::::::::: callout
+
+### M1 Users
+
+MacOS M1 users may need to ensure `libarchive` (from the conda-forge channel) has first been installed on their conda system before using mamba [^1]
+
+```bash
+conda remove -n base libarchive
+conda install -y -n base -c conda-forge \
+  libarchive 
+```
+
+::::::::::::::::::
+
 #### Create a conda virtual environment
 
 Create a virtual environment using conda
@@ -81,7 +95,12 @@ conda activate cwltutorial
 #### Install prerequisites via Mamba
 
 ```bash
-mamba install cwltool graphviz wget git nodejs
+mamba install --yes \
+  cwltool \
+  graphviz \
+  wget \
+  git \
+  nodejs
 ```
 
 :::::::::::::::: callout
@@ -93,7 +112,9 @@ The virtual environment needs to be activated every time you start a terminal us
 
 ::::::::::::::::
 
+[^1]: https://github.com/mamba-org/mamba/issues/1826#issuecomment-1196636463
+
 [vs_code]: https://code.visualstudio.com/
 [benten_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl
 [redhat_yaml_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml
-[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings
+[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings#_settingsjson

learners/files/windows_setup.Rmd

@@ -145,7 +145,7 @@ pip install cwltool
 [vs_code]: https://code.visualstudio.com/
 [benten_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=sbg-rabix.benten-cwl
 [redhat_yaml_vs_code_marketplace]: https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml
-[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings
+[user_settings_json]: https://code.visualstudio.com/docs/getstarted/settings#_settingsjson
 [wsl_installation_instructions]: https://learn.microsoft.com/en-us/windows/wsl/install
 [getting_started_with_wsl2]: https://medium.com/@awlucattini_60867/getting-started-with-wsl2-c11826654776?source=friends_link&sk=ddd411c0794ba2fce877984c300882ae
 [windows_docker_desktop_installation_page]: https://docs.docker.com/desktop/install/windows-install/