Merge pull request #4645 from bebatut/amr-detection-isolate

Reshape AMR detection tutorials and prepare learning pathway for AMR detection

FUNDERS.yaml

@@ -238,6 +238,14 @@ eurosciencegateway:
     funding_statement: |
         EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
 
+abromics:
+    name: ABRomics
+    github: false
+    joined: 2024-01
+    avatar: "/training-material/assets/images/abromics.png"
+    url: https://www.abromics.fr/
+    funder: true
+
 fnso2019:
     name: "OpenMetaPaper"
     short_name: "FNSO"

bin/lint.rb

@@ -559,6 +559,24 @@ def self.no_target_blank(contents)
     end
   end
 
+  def self.empty_alt_text(contents)
+    find_matching_texts(contents, /!\[\]\(/i)
+      .map do |idx, _text, selected|
+      path = selected[1].to_s.strip
+      if !File.exist?(path.gsub(%r{^/}, ''))
+        ReviewDogEmitter.error(
+          path: @path,
+          idx: idx,
+          match_start: selected.begin(0),
+          match_end: selected.end(0),
+          replacement: nil,
+          message: 'The alt text for this image seems to be empty',
+          code: 'GTN:034'
+        )
+      end
+    end
+  end
+
   def self.check_bad_link(contents)
     find_matching_texts(contents, /{%\s*link\s+([^%]*)\s*%}/i)
       .map do |idx, _text, selected|
@@ -575,6 +593,22 @@ def self.check_bad_link(contents)
         )
       end
     end
+
+    find_matching_texts(contents, /\]\(\)/i)
+      .map do |idx, _text, selected|
+      path = selected[1].to_s.strip
+      if !File.exist?(path.gsub(%r{^/}, ''))
+        ReviewDogEmitter.error(
+          path: @path,
+          idx: idx,
+          match_start: selected.begin(0),
+          match_end: selected.end(0),
+          replacement: nil,
+          message: 'The link does not seem to have a target.',
+          code: 'GTN:018'
+        )
+      end
+    end
   end
 
   def self.check_looks_like_heading(contents)
@@ -754,7 +788,8 @@ def self.fix_md(contents)
       *check_bad_heading_order(contents),
       *check_bolded_heading(contents),
       *snippets_too_close_together(contents),
-      *zenodo_api(contents)
+      *zenodo_api(contents),
+      *empty_alt_text(contents)
     ]
   end
 

learning-pathways/amr-gene-detection.md

@@ -0,0 +1,55 @@
+---
+layout: learning-pathway
+title: Detection of AMR genes in bacterial genomes
+description: |
+  Learn how to identify AMR genes in bacterial genomes
+type: use
+tags: [amr, bacteria, microgalaxy, one-health]
+
+editorial_board:
+- bebatut
+funding:
+- abromics
+
+
+pathway:
+#  - section: "Module 1: Introduction"
+#    description: |
+#      General introduction to AMR detection
+#    #tutorials:
+#    #  - name: introduction
+#    #    topic: genome-annotation
+
+  - section: "Module: AMR gene detection in bacterial isolates (short reads)"
+    description: |
+      
+    tutorials:
+      - name: mrsa-illumina
+        topic: assembly
+      - name: amr-gene-detection
+        topic: genome-annotation
+
+#  - section: "Module 3: AMR gene detection in bacterial isolates (long reads)"
+#    description: |
+#      
+#    tutorials:
+#      - name: mrsa-nanopore
+#        topic: assembly
+#      - name: amr-gene-detection
+#        topic: genome-annotation
+#
+#  - section: "Module 4: AMR gene detection in bacterial isolates (long and short reads)"
+#    description: |
+#      
+#    tutorials:
+#      #- name: hybrid-assembly
+#      #  topic: assembly
+#      - name: amr-gene-detection
+#        topic: genome-annotation
+
+  - section: "Recommended follow-up tutorials"
+    tutorials:
+      - name: pathogen-detection-from-nanopore-foodborne-data
+        topic: microbiome
+
+---