Merge pull request #31 from sanger-tol/githubtesting1

Githubtesting1
sanger-tol · Oct 11, 2023 · a8bdffd · a8bdffd
2 parents 5d5f200 + ccc1a7e
commit a8bdffd
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 0 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -69,6 +69,11 @@ jobs:
           mkdir NT_database
           curl -L https://ftp.ncbi.nlm.nih.gov/blast/db/18S_fungal_sequences.tar.gz | tar -C NT_database -xzf -
 
+      - name: Download the subset of Diamond database
+        run: |
+          mkdir diamond
+          wget -c https://tolit.cog.sanger.ac.uk/test-data/resources/diamond/UP000000212_1234679_tax.dmnd -O diamond/UP000000212_1234679_tax.dmnd
+
       - 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
@@ -14,6 +14,8 @@ ncbi_taxonomy_path: /home/runner/work/ascc/ascc/ncbi_taxdump/
 ncbi_rankedlineage_path: /home/runner/work/ascc/ascc/ncbi_taxdump/rankedlineage.dmp
 busco_lineages_folder: /home/runner/work/ascc/ascc/busco_database/lineages
 fcs_gx_database_path: /home/runner/work/ascc/ascc/FCS_gx/
+diamond_uniprot_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd
+diamond_nr_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd
 seqkit:
   sliding: 6000
   window: 100000
diff --git a/subworkflows/local/yaml_input.nf b/subworkflows/local/yaml_input.nf
@@ -36,6 +36,8 @@ workflow YAML_INPUT {
                 ncbi_rankedlineage_path:                        ( data.ncbi_rankedlineage_path          )
                 busco_lineages_folder:                          ( data.busco_lineages_folder            )
                 seqkit_values                       :           ( data.seqkit                           )
+                diamond_uniprot_database_path:                  ( data.diamond_uniprot_database_path    )
+                diamond_nr_database_path:                       ( data.diamond_nr_database_path         )
 
         }
         .set{ group }
@@ -78,6 +80,8 @@ workflow YAML_INPUT {
     ncbi_rankedlineage_path          = group.ncbi_rankedlineage_path
     busco_lineages_folder            = group.busco_lineages_folder
     fcs_gx_database_path             = group.fcs_gx_database_path
+    diamond_uniprot_database_path    = group.diamond_uniprot_database_path
+    diamond_nr_database_path         = group.diamond_nr_database_path
     seqkit_sliding                   = seqkit.sliding_value
     seqkit_window                    = seqkit.window_value
     versions                         = ch_versions.ifEmpty(null)