add gx database to github test

sanger-tol · Oct 9, 2023 · 3920d9d · 3920d9d
1 parent a6ae9f4
commit 3920d9d
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -46,7 +46,7 @@ jobs:
           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

diff --git a/assets/github_testing/test.yaml b/assets/github_testing/test.yaml
@@ -13,6 +13,7 @@ nt_kraken_db_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/n
 ncbi_taxonomy_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/
 ncbi_rankedlineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp
 busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-03-14/lineages
+fcs_gx_database_path: /home/runner/work/ascc/ascc/FCS_gx/
 seqkit:
   sliding: 6000
   window: 100000