fix tests workflow gact

BU-ISCIII · Jan 2, 2025 · 1de6d7a · 1de6d7a
1 parent fb2c7ab
commit 1de6d7a
Showing 1 changed file with 22 additions and 4 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -6,7 +6,7 @@ on:
     push:
 
 jobs:
-  test_analyze_schema:
+  test_taranys:
     runs-on: ubuntu-latest
 
     steps:
@@ -19,19 +19,37 @@ jobs:
           activate-environment: taranys_env
           environment-file: environment.yml
 
-      - name: Verify Conda environment
+      - name: Verify conda environment
         run: conda env list
 
       - name: Activate env and install taranys
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate taranys_env
           python -m pip install .
+          
+      - name: Testing analyze schema allele
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate taranys_env
           taranys analyze-schema -i  test/MLST_listeria/analyze_schema -o analyze_schema_test  --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset
 
-      - name: Testing Reference allele
+      - name: Testing reference allele
         run: |
           source $CONDA/etc/profile.d/conda.sh
           conda activate taranys_env
           taranys reference-alleles -s test/MLST_listeria/reference_allele -o reference_allele_test --cpus 1 
-          
+          
+      - name: Testing allele calling
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate taranys_env
+          taranys reference-alleles -s analyze_schema_test/new_schema -o reference_allele --cpus 1 
+          taranys allele-calling --force --schema analyze_schema_test/new_schema --reference reference_allele --annotation analyze_schema_test/allele_annotation.tar.gz --output allele_calling_test --cpus 1 --snp --alignment test/samples_listeria/*.fasta
+
+      - name: Testing distance matrix
+        run: |
+            source $CONDA/etc/profile.d/conda.sh
+            conda activate taranys_env
+            mkdir distance_matrix_result
+            taranys distance-matrix --alleles allele_calling_test/allele_calling_match.csv --force --output distance_matrix_result