Instruction pages

docs/hello_nextflow/01_orientation.md

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+# Orientation
+
+## Tour of Gitpod
+
+If you haven't yet, log into the [![Nextflow Training GitPod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training), which provides a virtual machine with everything already set up for you. 
+
+In the Gitpod window, you'll see a terminal. Type the following command to switch to the folder of this training material:
+
+```bash
+cd /workspace/gitpod/hello-nextflow
+```
+
+Take a few minutes to familiarize yourself with the gitpod environment, especially the file explorer, file browser and terminal.
+
+
+## Pipeline data and scripts
+
+We provide all test data, code and accessory needed to work through this training module. To view a full list, run the following command in the Gitpod terminal:
+
+```bash
+tree /workspace/gitpod/hello-nextflow
+```
+
+You should see the following output:
+
+```bash
+hello-nextflow
+├── data
+│   ├── bam
+│       ├── reads_father.bam
+│       ├── reads_mother.bam
+│       └── reads_son.bam
+│   ├── intervals.list
+│   ├── ref.tar.gz
+│   ├── sample_bams.txt
+│   └── samplesheet.csv
+├── scripts
+│   ├── hello-gatk-1.nf
+│   ├── hello-gatk-2.nf
+│   ├── hello-gatk-3.nf
+│   ├── hello-gatk-4.nf
+│   ├── hello-gatk-5.nf
+│   ├── hello-gatk-6.nf
+│   ├── hello-world-1.nf
+│   ├── hello-world-2.nf
+│   ├── hello-world-3.nf
+│   ├── hello-world-4.nf
+│   ├── hello-world-5.nf
+│   ├── hello-world-6.nf
+│   ├── hello-world-7.nf
+│   └── hello-world-8.nf
+├── greetings.txt
+├── hello-gatk.nf
+├── hello-world.nf
+└── nextflow.config
+
+```
+
+### Description of contents
+
+**The `data` directory** contains the input data we'll use in Part 2: Hello GATK, which uses an example from genomics to demonstrate how to build a simple analysis pipeline. The data is described in detail in that section of the training. 
+
+**The `scripts` directory** contains the completed workflow scripts that result from each step of the tutorial and are intended to be used as a reference to check your work. The name and number in the filename correspond to the step of the relevant tutorial. For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World. 
+
+**The file `greetings.txt`** is a plain text file used to provide inputs in Part 1: Hello World. 
+
+**The file `hello-gatk.nf`** is a stub that serves as a starting point to Part 2: Hello GATK. In its initial state, it is NOT a functional workflow script. 
+
+**The file `hello-world.nf`** is a simple but fully functional workflow script that serves as a starting point to Part 1: Hello World.
+
+**The file `nextflow.config`** is a configuration file that sets minimal environment properties.
+

docs/hello_nextflow/index.md

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+---
+title: Introduction
+hide:
+    - toc
+---
+
+# Hello Nextflow
+
+### Audience & prerequisites
+- Beginners with Nextflow
+- Required: basic experience with command line and scripting
+- Some bioinformatics and genomics concepts will be introduced
+
+### Learning objectives
+This training module aims to build basic proficiency in the following areas: 
+
+- Nextflow language:
+    - practical use of core components (sufficient to build a simple multi-step workflow)
+    - awareness of next-step concepts such as operators and channel factories
+
+- CLI execution: 
+    - launch a Nextflow workflow locally
+    - find outputs (results)
+    - interpret log outputs
+    - troubleshoot basic issues
+
+## Run it in Gitpod
+
+To make it easier to run this tutorial, we prepared a Gitpod environment with everything you need to follow it. Gitpod provides a virtual machine with everything already set up for you, accessible from your web browser or your code editor (eg. VSCode). To start, click on the button below.
+
+[![Open in GitPod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
+
+From there, follow the step-by-step instructions in the following pages.