Merge branch 'main' into neoantigen

bin/workflows-fetch.rb

@@ -11,6 +11,7 @@ def request(url)
   request['Accept'] = 'application/json'
   req_options = {
     use_ssl: uri.scheme == 'https',
+    max_retries: 5,
   }
   Net::HTTP.start(uri.hostname, uri.port, req_options) do |http|
     http.request(request)
@@ -37,19 +38,32 @@ def fetch_workflows(server)
 end
 
 def fetch_workflowhub
-  projects = JSON.parse(request('https://workflowhub.eu/projects').body)
+
+  begin
+      projects = JSON.parse(request('https://workflowhub.eu/projects').body)
+
+      response = request('https://workflowhub.eu/workflows?filter[workflow_type]=galaxy')
+      data = JSON.parse(response.body)
+  rescue StandardError
+      puts "ERROR: cannot fetch from WorkflowHub"
+      return []
+  end
+
   project_mapping = projects['data'].to_h { |p| [p['id'], p['attributes']['title']] }
 
-  response = request('https://workflowhub.eu/workflows?filter[workflow_type]=galaxy')
-  data = JSON.parse(response.body)
   if !data['links']['next'].nil?
     puts 'ERROR: Cannot yet handle multiple pages'
     exit 42
   end
   puts "INFO: Fetching #{data['data'].length} workflows from WorkflowHub"
   data['data'].map.with_index do |w, _i|
     # {"id"=>"14", "type"=>"workflows", "attributes"=>{"title"=>"Cheminformatics - Docking"}, "links"=>{"self"=>"/workflows/14"}}
-    wf_info = JSON.parse(request("https://workflowhub.eu#{w['links']['self']}").body)
+    begin
+        wf_info = JSON.parse(request("https://workflowhub.eu#{w['links']['self']}").body)
+    rescue StandardError
+        puts "ERROR: cannont fetch from WorkflowHub"
+        return []
+    end
     creator_list = []
 
     creator0 = wf_info['data']['attributes']['creators'][0]

learning-pathways/metagenomics.md

@@ -41,19 +41,7 @@ pathway:
       - name: quality-control
         topic: sequence-analysis
 
-  - section: "Module 4: Assembly"
-    description: |
-        This module covers the following questions:
-        - Why metagenomic data should be assembled?
-        - What is the difference between co-assembly and individual assembly?
-        - What is the difference between reads, contigs and scaffolds?
-        - How tools based on De Bruijn graph work?
-        - How to assess the quality of metagenomic data assembly?
-    tutorials:
-      - name: metagenomics-assembly
-        topic: microbiome
-
-  - section: "Module 5: Community taxonomic profiling"
+  - section: "Module 4: Community taxonomic profiling"
     description: |
         This module covers the following questions:
         - Which species (or genera, families, ...) are present in my sample?
@@ -64,26 +52,38 @@ pathway:
     tutorials:
       - name: taxonomic-profiling
         topic: microbiome
-        #description: More theoretical tutorial
       - name: beer-data-analysis
         topic: microbiome
-        #description: Application tutorial
 
-  - section: "Module 6: Taxonomic binning"
+  - section: "Module 5: Community diversity"
+    description: |
+       This module covers the following questions:
+        - How many different taxons are present in my sample? How do I additionally take their relative abundance into account?
+        - How similar or how dissimilar are my samples in term of taxonomic diversity?
+        - What are the different metrics used to calculate the taxonomic diversity of my samples?
+    tutorials:
+      - name: diversity
+        topic: microbiome
+
+  - section: "Module 6: Assembly"
+    description: |
+        This module covers the following questions:
+        - Why metagenomic data should be assembled?
+        - What is the difference between co-assembly and individual assembly?
+        - What is the difference between reads, contigs and scaffolds?
+        - How tools based on De Bruijn graph work?
+        - How to assess the quality of metagenomic data assembly?
+    tutorials:
+      - name: metagenomics-assembly
+        topic: microbiome
+
+  - section: "Module 7: Taxonomic binning"
     description:  |
       This module covers the process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other.
     tutorials:
       - name: metagenomics-binning
         topic: microbiome
 
-
-  #- section: "Module 7: Community Biodiversity"
-  #  description:
-  #
-  #  tutorials:
-  #    - name: learner_participation_engagement
-  #      topic: microbiome
-
   - section: "Module 8: Applying concepts to metatranscriptomics data"
     description: |
         This module covers the following questions:
@@ -96,6 +96,8 @@ pathway:
 
   - section: "Recommended follow-up tutorials"
     tutorials:
+      - name: metaplasmidome_query
+        topic: microbiome
       - name: pathogen-detection-from-nanopore-foodborne-data
         topic: microbiome
 ---

metadata/workflowhub.yml

@@ -145,6 +145,7 @@ microbiome/general-tutorial/wgs-worklow: '1067'
 microbiome/lotus2-identifying-fungi/lotus2-fungi-workflow: '1366'
 microbiome/metagenomics-assembly/metagenomics-assembly-tutorial-workflow: '1103'
 microbiome/metagenomics-assembly/workflow-generate-dataset-for-assembly-tutorial: '1099'
+microbiome/metaplasmidome_query/metaplasmidome: '1380'
 microbiome/metatranscriptomics-short/workflow1-preprocessing: '1092'
 microbiome/metatranscriptomics-short/workflow2-community-profile: '1088'
 microbiome/metatranscriptomics-short/workflow3-functional-information: '1084'