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Add Hello nf-core training course #610
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1135a2b
Course structure
vdauwera 0f6b03e
Add contents
vdauwera 2d8f1a6
First section of hello nf-core
vdauwera 6998635
Merge branch 'master' into gvda-hello-nf-core
vdauwera f5ec9c5
Add section 2 materials + update index
vdauwera 4ec4bf8
small fix
vdauwera 5513168
tiny fix
vdauwera 11e2302
Add WoW Side Quest as a prelude
vdauwera cb0d5b3
Replace WoW case by Hello Nextflow original
vdauwera c40f120
fix modules location
vdauwera ef8c6e6
add greetings.csv input for nf-core
vdauwera 844dc04
change dir name for starting case
vdauwera 4dd4a30
original hello complete
vdauwera 6f7d94a
composable workflow is composable
vdauwera b8a283e
nf-core conversion of hello nextflow complete
vdauwera a35a86c
fix note formatting
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change compliant to compatible to avoid overselling
vdauwera 1e429db
fix numbers formatting
vdauwera 06fa7eb
a few more minor fixes
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minor fixes
vdauwera 7e933ce
Minor improvements to orientation and demo run section
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added schemas and example samplesheet details
vdauwera c403c48
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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# Orientation | ||
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## GitHub Codespaces | ||
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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. | ||
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If you have not yet done so, please go through the [Environment Setup](../../envsetup/) mini-course before going any further. | ||
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## Working directory | ||
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Throughout this training course, we'll be working in the `hello-nf-core/` directory. | ||
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Change directory now by running this command in the terminal: | ||
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```bash | ||
cd hello-nf-core/ | ||
``` | ||
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!!!tip | ||
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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: | ||
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```bash | ||
cd /workspaces/training/hello-nf-core | ||
``` | ||
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Now let's have a look at the contents of this directory. | ||
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## Materials provided | ||
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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. | ||
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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. | ||
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Here we generate a table of contents to the second level down: | ||
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```bash | ||
tree . -L 2 | ||
``` | ||
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If you run this inside `hello-nf-core`, you should see the following output: | ||
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```console title="Directory contents" | ||
. | ||
├── ... | ||
├── solutions | ||
│ ├── 1-... | ||
└── ... | ||
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X directories, Y files | ||
``` | ||
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**Here's a summary of what you should know to get started:** | ||
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- [...] | ||
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- **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, [...] | ||
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**Now, to begin the course, click on the arrow in the bottom right corner of this page.** |
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