Prototype of NF4 RNAseq mini-course

docs/nf4_science/rnaseq/00_orientation.md

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+# Orientation
+
+The training environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
+However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface.
+
+If you have not yet done so, please follow [this link](../../envsetup/) before going any further.
+
+## Materials provided
+
+Throughout this training course, we'll be working in the `nf4-science/rnaseq/` directory, which you need to move into when you open the training workspace.
+This directory contains all the code files, test data and accessory files you will need.
+
+Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the training workspace in the VSCode interface.
+Alternatively, you can use the `tree` command.
+Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.
+
+Here we generate a table of contents to the second level down:
+
+```bash
+tree . -L 2
+```
+
+If you run this inside `nf4-science/rnaseq`, you should see the following output:
+
+```console title="Directory contents"
+
+TODO
+
+```
+
+!!!note
+
+    Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course.
+    This is just meant to give you an overview.
+
+**Here's a summary of what you should know to get started:**
+
+- **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in.
+
+- **The file `nextflow.config`** is a configuration file that sets minimal environment properties.
+  You can ignore it for now.
+
+- **The `data` directory** contains input data and related resources:
+  - _A reference genome_ consisting of a small region of the human chromosome 20 (from hg19/b37) and its accessory files (index and known splice sites).
+  - _RNAseq data_ corresponding to **[contents]**, which have been subset to a **[region?]** to keep the file sizes small.
+
+_Completed workflows (solutions) will be added in the near future._
+
+<!-- COMMENTED OUT UNTIL SOLUTIONS ARE READY (need to redo them)
+- **The `solutions` directory** contains the completed workflow scripts that result from each step of the course.
+  They are intended to be used as a reference to check your work and troubleshoot any issues.
+  The name and number in the filename correspond to the step of the relevant part of the course.
+  For example, the file `genomics-1-4.nf` is the expected result of completing steps 1 through 4 of _Part 1: Per-sample variant calling_ using the `genomics-1.nf` workflow.
+-->
+
+!!!tip
+
+    If for whatever reason you move out of this directory, you can always run this command to return to it:
+
+    ```bash
+    cd /workspaces/training/nf4-science/rnaseq
+    ```
+
+Now, to begin the course, click on the arrow in the bottom right corner of this page.