add subtopics to microbial

galaxyproject · Mar 14, 2024 · fb450ac · fb450ac
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diff --git a/topics/microbiome/metadata.yaml b/topics/microbiome/metadata.yaml
@@ -29,3 +29,17 @@ references:
     title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences."
     link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885"
     summary: ""
+
+subtopics:
+  - id: intro
+    title: "Introduction"
+    description: "Start here if you are new to microbiome analyses in Galaxy."
+  - id: metabarcoding
+    title: "Metabarcoding / Amplicon analyses"
+    description: "Taxonomic characterisation of mixed samples using a single gene region."
+  - id: metagenomics
+    title: "Metagenomics"
+    description: "Taxonomic and functional characterisation of mixed samples using whole genome data."
+  - id: metatranscriptomics
+    title: "Metatranscriptomics"
+    description: "Taxonomic and functional characterisation of mixed samples using transcriptome data."
diff --git a/topics/microbiome/tutorials/beer-data-analysis/tutorial.md b/topics/microbiome/tutorials/beer-data-analysis/tutorial.md
@@ -18,6 +18,7 @@ key_points:
 - Yeast species but also contamination can be identified and visualized directly from the sequences using several bioinformatics tools
 - With its graphical interface, Galaxy makes it easy to use the needed bioinformatics tools
 - Beer microbiome is not just made of yeast and can be quite complex
+subtopic: metagenomics
 tags:
 - nanopore
 - beer

diff --git a/topics/microbiome/tutorials/general-tutorial/tutorial.md b/topics/microbiome/tutorials/general-tutorial/tutorial.md
@@ -21,6 +21,7 @@ key_points:
 contributors:
   - shiltemann
   - bebatut
+subtopic: intro
 tags:
   - microgalaxy
 redirect_from:

diff --git a/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md b/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md
@@ -35,6 +35,7 @@ contributions:
     - bebatut
   funding:
     - gallantries
+subtopic: metagenomics
 tags:
   - assembly
   - metagenomics

diff --git a/topics/microbiome/tutorials/metagenomics-binning/tutorial.md b/topics/microbiome/tutorials/metagenomics-binning/tutorial.md
@@ -26,6 +26,7 @@ contributions:
   authorship:
     - npechl
     - fpsom
+subtopic: metagenomics
 tags:
   - binning
   - metagenomics

diff --git a/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md b/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md
@@ -13,6 +13,7 @@ objectives:
 - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes
 - Visualise a community structure
 level: Introductory
+subtopic: metatranscriptomics
 tags:
 - metatranscriptomics
 - microgalaxy

diff --git a/topics/microbiome/tutorials/metatranscriptomics/tutorial.md b/topics/microbiome/tutorials/metatranscriptomics/tutorial.md
@@ -13,6 +13,7 @@ objectives:
 - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes
 - Visualise a community structure
 level: Introductory
+subtopic: metatranscriptomics
 tags:
 - metatranscriptomics
 - microgalaxy

diff --git a/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md b/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md
@@ -20,7 +20,10 @@ contributors:
   - shiltemann
   - bebatut
   - tnabtaf
+subtopic: metabarcoding
 tags:
+  - metabarcoding
+  - 16S
   - microgalaxy
 redirect_from:
   - /topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial

diff --git a/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md b/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md
@@ -20,7 +20,10 @@ contributors:
   - shiltemann
   - bebatut
   - tnabtaf
+subtopic: metabarcoding
 tags:
+  - metabarcoding
+  - 16S
   - microgalaxy
 redirect_from:
   - /topics/metagenomics/tutorials/mothur-miseq-sop/tutorial

diff --git a/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md b/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md
@@ -16,7 +16,10 @@ key_points:
 - We preprocessed Nanopore sequences in order to improve their quality
 contributors:
 - gallardoalba
+subtopic: metabarcoding
 tags:
+  - metabarcoding
+  - 16S
   - nanopore
   - microgalaxy
 redirect_from:

diff --git a/...icrobiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md b/...icrobiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md
@@ -2,6 +2,7 @@
 layout: tutorial_hands_on
 
 title: "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition"
+subtopic: metagenomics
 tags:
     - microgalaxy
     - Nanopore data analysis

diff --git a/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md b/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md
@@ -22,6 +22,7 @@ key_points:
 contributors:
   - willemdek11
   - shiltemann
+subtopic: metabarcoding
 tags:
   - nanopore
   - plasmids

diff --git a/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md b/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md
@@ -4,8 +4,10 @@ title: QIIME 2 Cancer Microbiome Intervention
 hands_on: external
 hands_on_url: "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#"
 time_estimation: 10H
+subtopic: metabarcoding
 tags:
-- metagenomics
+- metabarcoding
+- 16S
 - taxonomic profiling
 - diversity
 - microgalaxy

diff --git a/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md b/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md
@@ -26,6 +26,7 @@ contributions:
     - paulzierep
    funding:
     - gallantries
+subtopic: metagenomics
 tags:
 - metagenomics
 - taxonomic profiling
-Original file line number
+Diff line change
@@ Expand Up / @@ -26,6 +26,7 @@ contributions: @@
       authorship:
         - npechl
         - fpsom
+    subtopic: metagenomics
     tags:
       - binning
       - metagenomics
@@ Expand Down @@