Change homepage, YAML and readme to reflect metatranscriptomics

Cloud-SPAN · Jul 3, 2024 · a761a03 · a761a03
1 parent a5984c2
commit a761a03
Show file tree

Hide file tree

Showing 3 changed files with 18 additions and 22 deletions.
diff --git a/README.md b/README.md
@@ -1,25 +1,22 @@
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 
-# Metagenomics
-
-This hands-on, online course teaches data analysis for metagenomics projects. It is aimed at those with little or no experience of using high performance computing (HPC) for data analysis. In the course we will cover:
-- navigating file directories and using the command line
-- logging into a remote cloud instance
-- using common commands and running analysis programs in the command line
-- what is metagenomics?
-- following a metagenomics analysis workflow including:
-  - performing quality control on reads
-  - assembly of reads into a metagenome
-  - improving your assembly with polishing
-  - binning into species/metagenome-assembled genomes (MAGs)
-  - taxonomic assignment and functional annotation using your binned reads
+# Metatranscriptomics
+
+```{=html}
+<!---
+This hands-on, online course teaches data analysis for metagenomics projects. It is aimed at those with little or no experience of using high performance computing (HPC) for data analysis. In the course we will cover: - navigating file directories and using the command line - logging into a remote cloud instance - using common commands and running analysis programs in the command line - what is metagenomics? - following a metagenomics analysis workflow including: - performing quality control on reads - assembly of reads into a metagenome - improving your assembly with polishing - binning into species/metagenome-assembled genomes (MAGs) - taxonomic assignment and functional annotation using your binned reads
 
 The course is taught as a mixture of live coding, online lectures, self-study and drop-in sessions.
 
 ## Prerequisites
+
 This course assumes no prior experience with the tools covered in the workshop but learners are expected to have some familiarity with biological concepts, including the concept of genomes and microbiomes. Participants should bring their own laptops and plan to participate actively.
 
 To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop.
 
 ## Acknowledgments
-The site infrastructure is based on [The Carpentries](https://carpentries.org/). The first two lessons are based on our [Prenomics](https://cloud-span.github.io/prenomics00-intro/) course; the rest are based on our [Metagenomics](https://cloud-span.github.io/metagenomics00-overview/) course.
+
+The first two lessons are based on our [Prenomics](https://cloud-span.github.io/prenomics00-intro/) course; the rest are based on our [Metagenomics](https://cloud-span.github.io/metagenomics00-overview/) course.
+-->
+```
+New repo for metatranscriptomics course. 🚧 WIP 🚧
diff --git a/_quarto.yml b/_quarto.yml
@@ -6,14 +6,14 @@ project:
 #date-format: "YYYY"
 
 website:
-  google-analytics: "G-9HW51GYWMM"
+  #google-analytics: ""
   cookie-consent: true
-  title: "Cloud-SPAN Metagenomics"
+  title: "Cloud-SPAN Transcriptomics"
   favicon: images/cloud-span-icon.png
   page-navigation: true         # prev and next options at the bottom of each page
   back-to-top-navigation: true
   reader-mode: true  
-  repo-url: https://github.com/Cloud-SPAN/nerc-metagenomics-v2q
+  repo-url: https://github.com/Cloud-SPAN/metatranscriptomics
   repo-actions: [edit, issue]
   page-footer:
     left: |
@@ -35,7 +35,7 @@ website:
         href: https://twitter.com/SpanCloud
         aria-label: Quarto Twitter
       - icon: github
-        href: https://github.com/Cloud-SPAN/nerc-metagenomics-v2q
+        href: https://github.com/Cloud-SPAN/metatranscriptomics
         aria-label: Quarto GitHub
       # - icon: rss
       #   href: https://quarto.org/docs/blog/index.xml
@@ -140,7 +140,7 @@ format:
       margin-width: 230px     # 300px
       gutter-width: 1.5rem    # 1.5rem
     lang: en
-    keywords: metagenomics, cloud computing, AWS, command line tools, data analysis, environmental science, learning resource
+    keywords: transcriptomics, cloud computing, AWS, command line tools, data analysis, environmental science, learning resource
     license: CC BY
     appendix-style: none
     title-block-style: none

diff --git a/index.qmd b/index.qmd
@@ -1,6 +1,5 @@
 ---
-title: "Metagenomics"
-subtitle: "Environmental Applications"
+title: "Transcriptomics"
 # title-block-banner: true
 ---
 
@@ -48,7 +47,7 @@ The course will take place over three weeks and will combine live coding and tea
 ## Course Overview
 
 | Lesson                                                                                   | Overview                                                                                                                               |
-|------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|
+|-----------------------------|-------------------------------------------|
 | [Files and Directories](docs/lesson01-files-and-directories/index.qmd)                   | Learn about files and directories, log onto a cloud instance and get a basic introduction to the shell.                                |
 | [Using the Command Line](docs/lesson02-using-the-command-line/index.qmd)                 | Learn more about using the shell to navigate directories, manipulate and search files, and combine existing commands to do new things. |
 | [QC & Assembly](docs/lesson03-qc-assembly/index.qmd)                                     | How to quality control and assemble a genome.                                                                                          |