Merge pull request #19 from aineniamh/include-background-dev

Include background dev
aineniamh · Aug 22, 2024 · 8a9910f · 8a9910f
2 parents 96d3963 + a73d28d
commit 8a9910f
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/.github/workflows/squirrel.yml b/.github/workflows/squirrel.yml
@@ -27,7 +27,9 @@ jobs:
       - name: Run squirrel with test data
         run: squirrel squirrel/data/NC_063383.fasta 2>&1 | tee squirrel.log
       - name: Run squirrel phylo with test data
-        run: squirrel ./test/cI_test.fasta --clade cladei --run-phylo --outgroups 'JX878419' 2>&1 | tee squirrel_phylo.log
+        run: squirrel ./test/cI_test.with_og.fasta --clade cladei --run-phylo --outgroups 'JX878419' 2>&1 | tee squirrel_phylo.log
       - name: Run squirrel seq qc with test data
-        run: squirrel ./test/cI_test.fasta --clade cladei  --run-phylo --outgroups 'JX878419' --seq-qc --assembly-refs squirrel/data/ref_seq.fasta 2>&1 | tee squirrel_qc.log
+        run: squirrel ./test/cI_test.with_og.fasta --clade cladei  --run-phylo --outgroups 'JX878419' --seq-qc --assembly-refs squirrel/data/ref_seq.fasta 2>&1 | tee squirrel_qc.log
+      - name: Run squirrel --include-background with test data
+        run: squirrel ./test/cI_test.fasta --clade cladei  --run-phylo --include-background 2>&1 | tee squirrel_bg.log
 
diff --git a/test/cI_test.fasta b/test/cI_test.fasta
diff --git a/test/cI_test.no_og.fasta → test/cI_test.with_og.fasta b/test/cI_test.no_og.fasta → test/cI_test.with_og.fasta