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 3
+```
+
+If you run this inside `nf4-science/rnaseq`, you should see the following output:
+
+```console title="Directory contents"
+.
+├── data
+│   ├── genome.fa
+│   ├── paired-end.csv
+│   ├── reads
+│   │   ├── ENCSR000COQ1_1.fastq.gz
+│   │   ├── ENCSR000COQ1_2.fastq.gz
+│   │   ├── ENCSR000COQ2_1.fastq.gz
+│   │   ├── ENCSR000COQ2_2.fastq.gz
+│   │   ├── ENCSR000COR1_1.fastq.gz
+│   │   ├── ENCSR000COR1_2.fastq.gz
+│   │   ├── ENCSR000COR2_1.fastq.gz
+│   │   ├── ENCSR000COR2_2.fastq.gz
+│   │   ├── ENCSR000CPO1_1.fastq.gz
+│   │   ├── ENCSR000CPO1_2.fastq.gz
+│   │   ├── ENCSR000CPO2_1.fastq.gz
+│   │   └── ENCSR000CPO2_2.fastq.gz
+│   └── single-end.csv
+├── nextflow.config
+├── rnaseq.nf
+└── solutions
+    ├── modules
+    │   ├── fastqc.nf
+    │   ├── fastqc_pe.nf
+    │   ├── hisat2_align.nf
+    │   ├── hisat2_align_pe.nf
+    │   ├── multiqc.nf
+    │   ├── trim_galore.nf
+    │   └── trim_galore_pe.nf
+    ├── rnaseq-2.1.nf
+    ├── rnaseq-2.2.nf
+    ├── rnaseq-2.3.nf
+    ├── rnaseq-3.1.nf
+    ├── rnaseq-3.2.nf
+    └── rnaseq_pe-3.3.nf
+
+```
+
+!!!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 `rnaseq.nf` file** is the outline if the workflow script we will work to develop.
+
+- **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_ called `genome.fa` consisting of a small region of the human chromosome 20 (from hg19/b37).
+  - _RNAseq data_ that has been subset to a small region to keep the file sizes down, in the `reads/` directory.
+  - _CSV files_ listing the IDs and paths of the example data files, for processing in batches.
+
+- **The `solutions` directory** contains the completed workflow scripts and modules 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 number in the filename corresponds to the step of the relevant part of the course.
+
+!!!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.