claude workflow

Author: dragon-ai-agent

.github/workflows/claude.yml

@@ -31,7 +31,7 @@ jobs:
           fetch-depth: 1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v5
 
       - name: Install python tools
         run: |
@@ -79,10 +79,34 @@ jobs:
           allowed_tools: "Bash(*),FileEdit,Edit,MultiEdit,WebSearch,WebFetch,mcp__ols_mcp__search_all_ontologies,mcp__ols_mcp__get_terms_from_ontology"
 
           # Optional: Add custom instructions for Claude to customize its behavior for your project
-          # custom_instructions: |
-          #   Follow our coding standards
-          #   Ensure all new code has tests
-          #   Use TypeScript for new files
+          custom_instructions: |
+            REPO: ${{ github.repository }}
+            ISSUE NUMBER: ${{ github.event.issue.number }}
+            TITLE: ${{ github.event.issue.title }}
+            BODY: ${{ github.event.issue.body }}
+            AUTHOR: ${{ github.event.issue.user.login }}
+
+            First analyzer the user request. If it doesn't involve gene review, 
+
+            If the user asks for a gene review, you must perform the following steps:
+              
+            When reviewing a gene, first check if the relevant files are in place. To create the uniprot and goa files, and a stub review,
+            run `just fetch-gene SPECIES GENE`. Never initiate these yourself. If a GENE-deep-research.md is NOT already present, you
+            should first do extensive literature search and make one, being sure to include citations for all statements.
+
+            ALWAYS do a `just validate SPECIES GENE` before finishing. You must fix BOTH ERRORs and WARNINGs.
+
+            Make sure you use the correct uniprot code for SPECIES (unless this is a common species: human, worm, fly, rat, mouse)
+            And use the uniprot gene symbol
+
+            Make sure your commit also includes:
+
+            - GENE-goa.tsv and GENE-uniprot.txt (if you created these with `just fetch-gene`)
+            - GENE-deep-research.md (if this was not previously present)
+            - New publications in `publications/`
+            - any bioinformatics analyses
+
+            Make a PR at the end
           
           # Optional: Custom environment variables for Claude
           # claude_env: |