Check by restoring to an older version

Author: fcaretti

Diff for: .github/workflows/main.yml

@@ -31,26 +31,7 @@ jobs:
         snakefile: workflow/Snakefile
         args: "--lint"
 
-  Testing_cd:
-    runs-on: ubuntu-latest
-    needs: 
-      - Linting
-      - Formatting
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Change to .test directory
-      run: cd .test
-
-    - name: Test workflow
-      run: |
-        snakemake --directory '.test' --snakefile 'workflow/Snakefile' --dry-run --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp
-      working-directory: .test
-
-    - name: Test report
-      run: |
-        snakemake --directory '.test' --snakefile 'workflow/Snakefile' --report report.zip
-      working-directory: .test
+  
 
   Testing:
     runs-on: ubuntu-latest
@@ -73,6 +54,8 @@ jobs:
           ls -R
           echo "Listing contents of .test directory:"
           ls -R .test
+          echo "Listing contents of .test/config directory:"
+          ls -R .test/config
           echo "Listing contents of .test/data directory:"
           ls -R .test/data
     - name: Test report

Diff for: workflow/Snakefile

@@ -16,12 +16,14 @@ reference_dict = f"{reference}.dict"
 sample_files = glob.glob(os.path.join(data_folder, "*.bam"))
 samples = [os.path.basename(f).replace(".bam", "") for f in sample_files]
 
+read_groups = [f"results/grouped/{sample}.bam" for sample in samples]
+deduped_files = [f"results/dedup/{sample}.bam" for sample in samples]
 splitted_files = [f"results/split/{sample}.bam" for sample in samples]
 
 
 rule all:
     input:
-        splitted_files,
+        deduped_files,
         reference_idx,
         reference_dict,