From b1ba26b02e63b33921e878b22fef2afe2658dda3 Mon Sep 17 00:00:00 2001 From: FranBonath Date: Wed, 20 Mar 2024 14:29:52 +0100 Subject: [PATCH 1/5] improve index page of tools training --- .../nf_core_basic_training/index.md | 116 +++++++++--------- 1 file changed, 60 insertions(+), 56 deletions(-) diff --git a/src/content/docs/contributing/nf_core_basic_training/index.md b/src/content/docs/contributing/nf_core_basic_training/index.md index bacaf5404c..96945c70b9 100644 --- a/src/content/docs/contributing/nf_core_basic_training/index.md +++ b/src/content/docs/contributing/nf_core_basic_training/index.md @@ -3,7 +3,7 @@ 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? @@ -11,7 +11,7 @@ subtitle: A guide to create Nextflow pipelines using nf-core tools :::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. @@ -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 + +

+ + Chapter 1 - setup the GitPod environment + +

+ +The course is using gitpod in order to avoid the time expense for downloading and installing tools and data. + +

+ + Chapter 2 - Creating a new nf-core pipeline from the nf-core template + +

+ +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 + +

+ + Chapter 3 - Exploring the nf-core template files + +

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

+ + Chapter 4 - Adding a nf-core module to your pipeline + +

+

+ + Chapter 5 - Adding a local custom module to your pipeline + +

+

+ + Chapter 6 - Working with Nextflow schema + +

+

+ + Chapter 7 - Linting your modules + +

+ +:::note{title="Key nf-core tools commands"} - `nf-core create ` creates a pipeline from the nf-core template. - `nf-core lint` lints the pipeline code for things that must be completed. From 3838928d2f17e73a972f31290a6d6600407e01af Mon Sep 17 00:00:00 2001 From: FranBonath Date: Wed, 20 Mar 2024 15:13:42 +0100 Subject: [PATCH 2/5] adding page navigation for tools training --- .../nf_core_basic_training/add_custom_module.md | 9 +++++++++ .../nf_core_basic_training/add_nf_core_module.md | 9 +++++++++ .../nf_core_basic_training/gitpod_environment.md | 8 ++++++++ .../docs/contributing/nf_core_basic_training/index.md | 10 +++++----- .../nf_core_basic_training/linting_modules.md | 9 +++++++++ .../nf_core_basic_training/nf_core_create_tool.md | 9 +++++++++ .../contributing/nf_core_basic_training/nf_schema.md | 9 +++++++++ .../nf_core_basic_training/template_walk_through.md | 9 +++++++++ 8 files changed, 67 insertions(+), 5 deletions(-) diff --git a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md index 3812f9946c..e78c92cc6b 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md @@ -301,3 +301,12 @@ In the directory `exercise_6` you will find the custom script `print_hello.py`, ::: + +

+ + < go to Chapter 4 + + + go to Chapter 6 > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md index 110b68f77a..3612c0492f 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md @@ -452,3 +452,12 @@ comparison to simple nextflow pipeline from the basic Nextflow training would be ::: + +

+ + < go to Chapter 3 + + + go to Chapter 5 > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md index 511ee6dab8..fc36f7ebba 100644 --- a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md +++ b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md @@ -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. +

+ + < go to training index + + + go to Chapter 2 > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/index.md b/src/content/docs/contributing/nf_core_basic_training/index.md index 96945c70b9..48492afcac 100644 --- a/src/content/docs/contributing/nf_core_basic_training/index.md +++ b/src/content/docs/contributing/nf_core_basic_training/index.md @@ -59,7 +59,7 @@ c) Running the pipeline using the test profile d) Linting the pipeline

- + Chapter 3 - Exploring the nf-core template files

@@ -67,22 +67,22 @@ d) Linting the pipeline The template contains a range of important files and directories. This chapter is giving explanations to all the template content important to beginners.

- + Chapter 4 - Adding a nf-core module to your pipeline

- + Chapter 5 - Adding a local custom module to your pipeline

- + Chapter 6 - Working with Nextflow schema

- + Chapter 7 - Linting your modules

diff --git a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md index b80abf407f..2f627e29c0 100644 --- a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md +++ b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md @@ -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 ``` + +

+ + < go to Chapter 6 + + + go to training index > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md index 18debb141a..79846a01ad 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md @@ -357,3 +357,12 @@ nf-core lint ::: + +

+ + < go to Chapter 1 + + + go to Chapter 3 > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md index 4bde325e93..3c2e267ee6 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md @@ -62,3 +62,12 @@ Here in the schema editor you can edit: ::: + +

+ + < go to Chapter 5 + + + go to Chapter 7 > + +

diff --git a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md index 21f7d67f97..a24fea20cc 100644 --- a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md +++ b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md @@ -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] ::: + +

+ + < go to Chapter 2 + + + go to Chapter 4 > + +

From bedf765902f693da1ddc80ad2e74f1268d7d28a4 Mon Sep 17 00:00:00 2001 From: FranBonath Date: Wed, 20 Mar 2024 15:40:14 +0100 Subject: [PATCH 3/5] trying to fix links --- .../nf_core_basic_training/add_custom_module.md | 4 ++-- .../nf_core_basic_training/add_nf_core_module.md | 4 ++-- .../nf_core_basic_training/gitpod_environment.md | 4 ++-- .../contributing/nf_core_basic_training/index.md | 14 +++++++------- .../nf_core_basic_training/linting_modules.md | 4 ++-- .../nf_core_basic_training/nf_core_create_tool.md | 4 ++-- .../nf_core_basic_training/nf_schema.md | 4 ++-- .../template_walk_through.md | 4 ++-- 8 files changed, 21 insertions(+), 21 deletions(-) diff --git a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md index e78c92cc6b..a662e7461d 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md @@ -303,10 +303,10 @@ In the directory `exercise_6` you will find the custom script `print_hello.py`, :::

- + < go to Chapter 4 - + go to Chapter 6 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md index 3612c0492f..e814d7d6ec 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md @@ -454,10 +454,10 @@ comparison to simple nextflow pipeline from the basic Nextflow training would be :::

- + < go to Chapter 3 - + go to Chapter 5 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md index fc36f7ebba..5f2cf60e72 100644 --- a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md +++ b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md @@ -69,10 +69,10 @@ To save any file locally from the explorer panel, right-click the file and selec

- + < go to training index - + go to Chapter 2 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/index.md b/src/content/docs/contributing/nf_core_basic_training/index.md index 48492afcac..09b8a27dfb 100644 --- a/src/content/docs/contributing/nf_core_basic_training/index.md +++ b/src/content/docs/contributing/nf_core_basic_training/index.md @@ -35,7 +35,7 @@ This training can be followed either based on this documentation alone, or via a ## Training sessions

- + Chapter 1 - setup the GitPod environment

@@ -43,7 +43,7 @@ This training can be followed either based on this documentation alone, or via a The course is using gitpod in order to avoid the time expense for downloading and installing tools and data.

- + Chapter 2 - Creating a new nf-core pipeline from the nf-core template

@@ -59,7 +59,7 @@ c) Running the pipeline using the test profile d) Linting the pipeline

- + Chapter 3 - Exploring the nf-core template files

@@ -67,22 +67,22 @@ d) Linting the pipeline The template contains a range of important files and directories. This chapter is giving explanations to all the template content important to beginners.

- + Chapter 4 - Adding a nf-core module to your pipeline

- + Chapter 5 - Adding a local custom module to your pipeline

- + Chapter 6 - Working with Nextflow schema

- + Chapter 7 - Linting your modules

diff --git a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md index 2f627e29c0..8aa11dfb67 100644 --- a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md +++ b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md @@ -14,10 +14,10 @@ nf-core modules lint --all ```

- + < go to Chapter 6 - + go to training index >

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md index 79846a01ad..e15da678ac 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md @@ -359,10 +359,10 @@ nf-core lint :::

- + < go to Chapter 1 - + go to Chapter 3 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md index 3c2e267ee6..1c3a4b42af 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md @@ -64,10 +64,10 @@ Here in the schema editor you can edit: :::

- + < go to Chapter 5 - + go to Chapter 7 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md index a24fea20cc..2f2b74b021 100644 --- a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md +++ b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md @@ -198,10 +198,10 @@ This file keeps track of modules installed using nf-core tools from the nf-core/ :::

- + < go to Chapter 2 - + go to Chapter 4 >

From 7e76f2bad942b6850ac27b5d5fc954a6edc376f6 Mon Sep 17 00:00:00 2001 From: FranBonath Date: Wed, 20 Mar 2024 15:53:55 +0100 Subject: [PATCH 4/5] trying to fix links II --- .../nf_core_basic_training/add_custom_module.md | 4 ++-- .../nf_core_basic_training/add_nf_core_module.md | 4 ++-- .../nf_core_basic_training/gitpod_environment.md | 4 ++-- .../contributing/nf_core_basic_training/index.md | 14 +++++++------- .../nf_core_basic_training/linting_modules.md | 4 ++-- .../nf_core_basic_training/nf_core_create_tool.md | 4 ++-- .../nf_core_basic_training/nf_schema.md | 4 ++-- .../template_walk_through.md | 4 ++-- 8 files changed, 21 insertions(+), 21 deletions(-) diff --git a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md index a662e7461d..065de1c8ad 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_custom_module.md @@ -303,10 +303,10 @@ In the directory `exercise_6` you will find the custom script `print_hello.py`, :::

- + < go to Chapter 4 - + go to Chapter 6 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md index e814d7d6ec..9a56a6a547 100644 --- a/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md +++ b/src/content/docs/contributing/nf_core_basic_training/add_nf_core_module.md @@ -454,10 +454,10 @@ comparison to simple nextflow pipeline from the basic Nextflow training would be :::

- + < go to Chapter 3 - + go to Chapter 5 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md index 5f2cf60e72..8e71bad01f 100644 --- a/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md +++ b/src/content/docs/contributing/nf_core_basic_training/gitpod_environment.md @@ -69,10 +69,10 @@ To save any file locally from the explorer panel, right-click the file and selec

- + < go to training index - + go to Chapter 2 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/index.md b/src/content/docs/contributing/nf_core_basic_training/index.md index 09b8a27dfb..8f313f77a9 100644 --- a/src/content/docs/contributing/nf_core_basic_training/index.md +++ b/src/content/docs/contributing/nf_core_basic_training/index.md @@ -35,7 +35,7 @@ This training can be followed either based on this documentation alone, or via a ## Training sessions

- + Chapter 1 - setup the GitPod environment

@@ -43,7 +43,7 @@ This training can be followed either based on this documentation alone, or via a The course is using gitpod in order to avoid the time expense for downloading and installing tools and data.

- + Chapter 2 - Creating a new nf-core pipeline from the nf-core template

@@ -59,7 +59,7 @@ c) Running the pipeline using the test profile d) Linting the pipeline

- + Chapter 3 - Exploring the nf-core template files

@@ -67,22 +67,22 @@ d) Linting the pipeline The template contains a range of important files and directories. This chapter is giving explanations to all the template content important to beginners.

- + Chapter 4 - Adding a nf-core module to your pipeline

- + Chapter 5 - Adding a local custom module to your pipeline

- + Chapter 6 - Working with Nextflow schema

- + Chapter 7 - Linting your modules

diff --git a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md index 8aa11dfb67..9721bc8465 100644 --- a/src/content/docs/contributing/nf_core_basic_training/linting_modules.md +++ b/src/content/docs/contributing/nf_core_basic_training/linting_modules.md @@ -14,10 +14,10 @@ nf-core modules lint --all ```

- + < go to Chapter 6 - + go to training index >

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md index e15da678ac..c869a78453 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_core_create_tool.md @@ -359,10 +359,10 @@ nf-core lint :::

- + < go to Chapter 1 - + go to Chapter 3 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md index 1c3a4b42af..7208d3fa6d 100644 --- a/src/content/docs/contributing/nf_core_basic_training/nf_schema.md +++ b/src/content/docs/contributing/nf_core_basic_training/nf_schema.md @@ -64,10 +64,10 @@ Here in the schema editor you can edit: :::

- + < go to Chapter 5 - + go to Chapter 7 >

diff --git a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md index 2f2b74b021..bb0427266a 100644 --- a/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md +++ b/src/content/docs/contributing/nf_core_basic_training/template_walk_through.md @@ -198,10 +198,10 @@ This file keeps track of modules installed using nf-core tools from the nf-core/ :::

- + < go to Chapter 2 - + go to Chapter 4 >

From 06b5eb19457e34cb54b1ec5964384fb1a3175a6a Mon Sep 17 00:00:00 2001 From: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Date: Wed, 20 Mar 2024 16:21:56 +0100 Subject: [PATCH 5/5] Update src/content/docs/contributing/nf_core_basic_training/index.md Co-authored-by: Mahesh Binzer-Panchal --- src/content/docs/contributing/nf_core_basic_training/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/docs/contributing/nf_core_basic_training/index.md b/src/content/docs/contributing/nf_core_basic_training/index.md index 8f313f77a9..9a0a5dc15a 100644 --- a/src/content/docs/contributing/nf_core_basic_training/index.md +++ b/src/content/docs/contributing/nf_core_basic_training/index.md @@ -40,7 +40,7 @@ This training can be followed either based on this documentation alone, or via a

-The course is using gitpod in order to avoid the time expense for downloading and installing tools and data. +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.