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1135a2b
Course structure
vdauwera May 9, 2025
0f6b03e
Add contents
vdauwera May 10, 2025
2d8f1a6
First section of hello nf-core
vdauwera May 10, 2025
6998635
Merge branch 'master' into gvda-hello-nf-core
vdauwera May 11, 2025
f5ec9c5
Add section 2 materials + update index
vdauwera May 12, 2025
4ec4bf8
small fix
vdauwera May 12, 2025
5513168
tiny fix
vdauwera May 12, 2025
11e2302
Add WoW Side Quest as a prelude
vdauwera May 12, 2025
cb0d5b3
Replace WoW case by Hello Nextflow original
vdauwera May 12, 2025
c40f120
fix modules location
vdauwera May 12, 2025
ef8c6e6
add greetings.csv input for nf-core
vdauwera May 12, 2025
844dc04
change dir name for starting case
vdauwera May 12, 2025
4dd4a30
original hello complete
vdauwera May 12, 2025
6f7d94a
composable workflow is composable
vdauwera May 13, 2025
b8a283e
nf-core conversion of hello nextflow complete
vdauwera May 13, 2025
a35a86c
fix note formatting
vdauwera May 13, 2025
0c43c02
change compliant to compatible to avoid overselling
vdauwera May 13, 2025
1e429db
fix numbers formatting
vdauwera May 13, 2025
06fa7eb
a few more minor fixes
vdauwera May 13, 2025
f7b512c
minor fixes
vdauwera May 13, 2025
7e933ce
Minor improvements to orientation and demo run section
vdauwera May 14, 2025
e6c3fc8
added schemas and example samplesheet details
vdauwera May 14, 2025
c403c48
Improved Hello rewrite
vdauwera May 14, 2025
03a6104
deleting due to weirdness
vdauwera May 14, 2025
2f72b53
Start and end states of core-hello (minus the git file)
vdauwera May 14, 2025
95db085
Improvements based on Summit trial run
vdauwera Jun 3, 2025
e95bc18
fixed headings
vdauwera Jun 3, 2025
ce429c0
Apply suggestions from Ken's code review
vdauwera Jun 4, 2025
dabcc5d
caught a straggler
vdauwera Jun 4, 2025
c4b37e0
prettier fix
vdauwera Jun 4, 2025
d75633d
Merge branch 'master' into gvda-hello-nf-core
vdauwera Jun 4, 2025
220e200
note formatting fix
vdauwera Jun 4, 2025
edba0a3
Merge branch 'gvda-hello-nf-core' of https://github.com/nextflow-io/t…
vdauwera Jun 4, 2025
a8d5142
Improve meta pages (especially next steps)
vdauwera Jun 4, 2025
5a8e113
Add survey page for hello nf-core
vdauwera Jun 4, 2025
b08d71f
Improve next steps pages
vdauwera Jun 4, 2025
70cd57c
Add next steps page to Genomics course too
vdauwera Jun 4, 2025
fb70c7f
Add logo to index page
vdauwera Jun 4, 2025
788b6d3
formatting fixes
vdauwera Jun 4, 2025
bffe780
formatting sub lists...
vdauwera Jun 4, 2025
c5ed364
nested lists fix?
vdauwera Jun 4, 2025
50a6843
workaround for nested lists not formatting correctly
vdauwera Jun 4, 2025
ea70e94
aaaargh
vdauwera Jun 4, 2025
98cdfa7
alternate attempt to previous
vdauwera Jun 4, 2025
7dd20f7
least objectionable workaround
vdauwera Jun 4, 2025
88213b3
a few more tweaks
vdauwera Jun 4, 2025
d62f157
Merge branch 'master' into gvda-hello-nf-core
vdauwera Jun 4, 2025
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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.

## 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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