add gx test data to github

sanger-tol · Oct 9, 2023 · fe3c71f · fe3c71f
1 parent 6d5c232
commit fe3c71f
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -40,6 +40,15 @@ jobs:
         run: |
           curl https://tolit.cog.sanger.ac.uk/test-data/resources/ascc/asccTinyTest.tar.gz | tar xzf -
 
+      - name: Download the FCS-gx database
+        run: |
+          mkdir FCS_gx
+          wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.taxa.tsv -O FCS_gx/test-only.taxa.tsv
+          wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxi -O FCS_gx/test-only.gxi
+          wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxs -O FCS_gx/test-only.gxs
+          wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.meta.jsonl -O FCS_gx/test-only.meta.jsonl
+          wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz -O FCS_gx/test-only.blast_div.tsv.gz
+          pwd
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters