Update NF4 Genomics course description and main filenames

nextflow-io · Feb 5, 2025 · 8eb6291 · 8eb6291
1 parent e8b97ae
commit 8eb6291
Show file tree

Hide file tree

Showing 6 changed files with 25 additions and 15 deletions.
diff --git a/docs/nf4_genomics/01_orientation.md → docs/nf4_genomics/00_orientation.md b/docs/nf4_genomics/01_orientation.md → docs/nf4_genomics/00_orientation.md
diff --git a/docs/nf4_genomics/02_linear.md → ...genomics/01_per_sample_variant_calling.md b/docs/nf4_genomics/02_linear.md → ...genomics/01_per_sample_variant_calling.md
@@ -1,4 +1,4 @@
-# Part 3: Hello Genomics
+# Part 1: Per-sample variant calling
 
 In Part 1, you learned how to use the basic building blocks of Nextflow to assemble a simple pipeline capable of processing some text and parallelizing execution if there were multiple inputs.
 Then in Part 2, you learned how to use containers to pull in command line tools to test them and integrate them into your pipelines without having to deal with software dependency issues.

diff --git a/docs/nf4_genomics/03_collect.md → docs/nf4_genomics/02_joint_calling.md b/docs/nf4_genomics/03_collect.md → docs/nf4_genomics/02_joint_calling.md
@@ -1,4 +1,4 @@
-# Part 4: Hello Operators
+# Part 2: Joint calling on a cohort
 
 In Part 3, you built a pipeline that was completely linear and processed each sample's data independently of the others.
 However, in real pipelines, you may need to combine data from multiple samples, or combine different kinds of data.

diff --git a/docs/nf4_genomics/04_config.md → docs/nf4_genomics/03_configuration.md b/docs/nf4_genomics/04_config.md → docs/nf4_genomics/03_configuration.md
diff --git a/docs/nf4_genomics/05_testing.md → docs/nf4_genomics/04_testing.md b/docs/nf4_genomics/05_testing.md → docs/nf4_genomics/04_testing.md
diff --git a/docs/nf4_genomics/index.md b/docs/nf4_genomics/index.md
@@ -6,26 +6,36 @@ hide:
 
 # Nextflow for Genomics
 
-[TODO]]
-
-Let's get started!
-
-[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
+This training course is intended for researchers in genomics and related fields who are interested in developing or customizing data analysis pipelines.
+It builds on the [Hello Nextflow](TODO) beginner training and demonstrates how to use Nextflow in the specific context of the genomics domain.
 
 ## Learning objectives
 
-In this workshop, you will learn [TODO].
+By working through this course, you will learn how to apply foundational Nextflow concepts and tooling to a typical genomics use case.
 
 By the end of this workshop you will be able to:
 
-[TODO]
+-   Write a linear workflow to apply variant calling to a single sample
+-   Handle accessory files such as index files and reference genome resources appropriately
+-   Leverage Nextflow's dataflow paradigm to parallelize per-sample variant calling
+-   Implement multi-sample variant calling using relevant channel operators
+-   Configure pipeline execution and manage and optimize resource allocations
+-   Implement per-step and end-to-end pipeline tests that handle genomics-specific idiosyncrasies appropriately
+
+<!-- TODO for future expansion: add metadata/samplesheet handling -->
 
-## Audience & prerequisites
+## Prerequisites
 
-[TODO]
+The course assumes some minimal familiarity with the following:
 
-**Prerequisites**
+-   Tools and file formats commonly used in this scientific domain
+-   Experience with the command line
+-   Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../hello_nextflow/index.md) beginner training.
 
--   A GitHub account
--   Experience with command line
-    [TODO]
+For technical requirements and environment setup, see the [Environment Setup](../envsetup/index.md) mini-course.
+
+## Get started
+
+To get started, open the training environment by clicking the 'Open in Gitpod' button below.
+
+[![Open in Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)