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page navigations for tools training #2397

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page navigations for tools training #2397

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b1ba26b
improve index page of tools training
FranBonath Mar 20, 2024
3838928
adding page navigation for tools training
FranBonath Mar 20, 2024
bedf765
trying to fix links
FranBonath Mar 20, 2024
7e76f2b
trying to fix links II
FranBonath Mar 20, 2024
06b5eb1
Update src/content/docs/contributing/nf_core_basic_training/index.md
FranBonath Mar 20, 2024
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9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/add_custom_module.md
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Expand Up @@ -301,3 +301,12 @@ In the directory `exercise_6` you will find the custom script `print_hello.py`,
</details>

:::

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/add_nf_core_module/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 4
</a>
<a href="/docs/contributing/nf_core_basic_training/nf_schema/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 6 >
</a>
</p>
9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md
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Expand Up @@ -452,3 +452,12 @@ comparison to simple nextflow pipeline from the basic Nextflow training would be
</details>

:::

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/template_walk_through/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 3
</a>
<a href="/docs/contributing/nf_core_basic_training/add_custom_module/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 5 >
</a>
</p>
8 changes: 8 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md
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Expand Up @@ -68,3 +68,11 @@ If you have lost your environment, you can find the main scripts used in this tu
To save any file locally from the explorer panel, right-click the file and select Download.

</details>
<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to training index
</a>
<a href="/docs/contributing/nf_core_basic_training/nf_core_create_tool/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 2 >
</a>
</p>
116 changes: 60 additions & 56 deletions src/content/docs/contributing/nf_core_basic_training/index.md
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Expand Up @@ -3,15 +3,15 @@ title: Basic training to create an nf-core pipeline
subtitle: A guide to create Nextflow pipelines using nf-core tools
---

## Scope
# Scope

- How do I create a pipeline using nf-core tools?
- How do I incorporate modules from nf-core modules?
- How can I use custom code in my pipeline?

:::note

### Learning objectives
## Learning objectives

- The learner will create a simple pipeline using the nf-core template.
- The learner will identify key files in the pipeline.
Expand All @@ -24,66 +24,70 @@ subtitle: A guide to create Nextflow pipelines using nf-core tools

This training course aims to demonstrate how to build an nf-core pipeline using the nf-core pipeline template and nf-core modules and subworkflows as well as custom, local modules. Be aware that we are not going to explain any fundamental Nextflow concepts, as such we advise anyone taking this course to have completed the [Basic Nextflow Training Workshop](https://training.nextflow.io/).

```md
During this course we are going to build a Simple RNA-Seq workflow.
This workflow is by no means ment to be a useful bioinformatics workflow,
but should only teach the objectives of the course, so please,
**DO NOT use this workflow to analyse RNA sequencing data**!
```
# Let's get started

### Follow the training videos
## Follow the training videos

This training can be followed either based on this documentation alone, or via a training video hosted on youtube. You can find the youtube video in the Youtube playlist below:

(no such video yet)

## Overview

### Layout of the pipeline

The course is going to build an (totally unscientific and useless) RNA seq pipeline that does the following:

1. Indexing of a transcriptome file
2. Quality control
3. Quantification of transcripts
4. [whatever the custom script does]
5. Generation of a MultiQC report

### Let's get started

1. **Setting up the gitpod environment for the course**

The course is using gitpod in order to avoid the time expense for downloading and installing tools and data. [Learn how to setup the GitPod environment](/docs/contributing/nf_core_basic_training/gitpod_environment.md)

2. **Creating a new nf-core pipeline from the nf-core template**

a) generate the pipeline with `nf-core create`

b) The template git repository

c) Running the pipeline using the test profile

d) Linting the pipeline

[These steps are described in the section "Generate a pipeline with nf-core tools"](/docs/contributing/nf_core_basic_training/nf_core_create_tool.md)

3. **Exploring the nf-core template files**

The template contains a range of important files and directories. Check them out in the [walk-through of the template files](/docs/contributing/nf_core_basic_training/template_walk_through.md)

4. **Building a nf-core pipeline using the template**

a) [Adding a nf-core module to your pipeline](/docs/contributing/nf_core_basic_training/add_nf_core_module.md)

b) [Adding a local custom module to your pipeline](/docs/contributing/nf_core_basic_training/add_custom_module.md)

c) [Working with Nextflow schema](/docs/contributing/nf_core_basic_training/nf_schema.md)

d) [Linting your modules](/docs/contributing/nf_core_basic_training/linting_modules.md)

:::note

### Key points
## Training sessions

<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/gitpod_environment/" class="btn btn-lg btn-success" target="_blank">
Chapter 1 - setup the GitPod environment
</a>
</p>

This course uses [Gitpod](https://www.gitpod.io/) in order to avoid spending time downloading and installing tools and data. All necessary tools and data should be available in the Gitpod environment.

<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/nf_core_create_tool/" class="btn btn-lg btn-success" target="_blank">
Chapter 2 - Creating a new nf-core pipeline from the nf-core template
</a>
</p>

This includes the following sub-sections:

a) generate the pipeline with `nf-core create`

b) The template git repository

c) Running the pipeline using the test profile

d) Linting the pipeline

<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/nf_core_create_tool/" class="btn btn-lg btn-success">
Chapter 3 - Exploring the nf-core template files
</a>
</p>

The template contains a range of important files and directories. This chapter is giving explanations to all the template content important to beginners.

<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/add_nf_core_module/" class="btn btn-lg btn-success">
Chapter 4 - Adding a nf-core module to your pipeline
</a>
</p>
<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/add_custom_module/" class="btn btn-lg btn-success">
Chapter 5 - Adding a local custom module to your pipeline
</a>
</p>
<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/nf_schema/" class="btn btn-lg btn-success">
Chapter 6 - Working with Nextflow schema
</a>
</p>
<p class="text-left">
<a href="/docs/contributing/nf_core_basic_training/linting_modules/" class="btn btn-lg btn-success">
Chapter 7 - Linting your modules
</a>
</p>

:::note{title="Key nf-core tools commands"}
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This should probably be moved to the relevant sections.

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I thought it was quite nice to have the main commands on the title page...

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Maybe add a header then so it has it's own section. Command summary or something.


- `nf-core create <pipeline>` creates a pipeline from the nf-core template.
- `nf-core lint` lints the pipeline code for things that must be completed.
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9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/linting_modules.md
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Expand Up @@ -12,3 +12,12 @@ As well as the pipeline template you can lint individual or all modules with a s
nf-core modules lint --all

```

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/nf_schema/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 6
</a>
<a href="/docs/contributing/nf_core_basic_training/index/" class="btn btn-lg btn-success" style="font-size: 14px">
go to training index >
</a>
</p>
9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md
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Expand Up @@ -357,3 +357,12 @@ nf-core lint
</details>

:::

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/gitpod_environment/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 1
</a>
<a href="/docs/contributing/nf_core_basic_training/template_walk_through/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 3 >
</a>
</p>
9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/nf_schema.md
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Expand Up @@ -62,3 +62,12 @@ Here in the schema editor you can edit:
</details>

:::

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/add_custom_module/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 5
</a>
<a href="/docs/contributing/nf_core_basic_training/linting_modules/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 7 >
</a>
</p>
9 changes: 9 additions & 0 deletions src/content/docs/contributing/nf_core_basic_training/template_walk_through.md
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Expand Up @@ -196,3 +196,12 @@ This file keeps track of modules installed using nf-core tools from the nf-core/

[MORE QUESTIONS CAN BE ADDED HERE]
:::

<p class="text-center">
<a href="/docs/contributing/nf_core_basic_training/nf_core_create_tool/" class="btn btn-lg btn-success" style="font-size: 14px">
< go to Chapter 2
</a>
<a href="/docs/contributing/nf_core_basic_training/add_nf_core_module/" class="btn btn-lg btn-success" style="font-size: 14px">
go to Chapter 4 >
</a>
</p>
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