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1135a2b
Course structure
vdauwera May 9, 2025
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Add contents
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First section of hello nf-core
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Merge branch 'master' into gvda-hello-nf-core
vdauwera May 11, 2025
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Add section 2 materials + update index
vdauwera May 12, 2025
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small fix
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tiny fix
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Add WoW Side Quest as a prelude
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Replace WoW case by Hello Nextflow original
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fix modules location
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add greetings.csv input for nf-core
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change dir name for starting case
vdauwera May 12, 2025
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original hello complete
vdauwera May 12, 2025
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composable workflow is composable
vdauwera May 13, 2025
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nf-core conversion of hello nextflow complete
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fix note formatting
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change compliant to compatible to avoid overselling
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fix numbers formatting
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a few more minor fixes
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minor fixes
vdauwera May 13, 2025
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Minor improvements to orientation and demo run section
vdauwera May 14, 2025
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added schemas and example samplesheet details
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Improved Hello rewrite
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deleting due to weirdness
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Start and end states of core-hello (minus the git file)
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64 changes: 64 additions & 0 deletions docs/hello_nf-core/00_orientation.md
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# Orientation

## GitHub Codespaces

The GitHub Codespaces 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) GitHub 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 go through the [Environment Setup](../../envsetup/) mini-course before going any further.

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!!! warning
This training is designed for nf-core tools version 3.2.1, which should be the version installed in the codespace. If you use a different version of nf-core tooling you may have difficulty following along.
You can check what version is installed using the command`nf-core --version`.

## Working directory

Throughout this training course, we'll be working in the `hello-nf-core/` directory.

Change directory now by running this command in the terminal:

```bash
cd hello-nf-core/
```

!!!tip

If for whatever reason you move out of this directory, you can always use the full path to return to it, assuming you're running this within the Github Codespaces training environment:

```bash
cd /workspaces/training/hello-nf-core
```

Now let's have a look at the contents of this directory.

## Materials provided

You can explore the contents of this directory by using the file explorer on the left-hand side of the training workspace.
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 `hello-nf-core`, you should see the following output:

```console title="Directory contents"
.
├── ...
├── solutions
│ ├── 1-...
└── ...

X directories, Y files
```

**Here's a summary of what you should know to get started:**

- [...]

- **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, [...]

**Now, to begin the course, click on the arrow in the bottom right corner of this page.**
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