fix: remove -r flag (#624)

* remove -r flag

* fix

.github/workflows/main.yml

@@ -69,7 +69,7 @@ jobs:
       #- Pre-Commit
     strategy:
       matrix:
-        rule: [all, all -npr]
+        rule: [all, all -np]
         # disable ont actions
         technology: [all, illumina, ont, ion]
         # technology: [all, illumina, ion]
@@ -141,26 +141,26 @@ jobs:
         with:
           directory: .tests
           snakefile: workflow/Snakefile
-          args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
+          args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
 
       - name: Test report
         uses: snakemake/[email protected]
-        if: startsWith(matrix.rule, 'all -npr') != true
+        if: startsWith(matrix.rule, 'all -np') != true
         with:
           directory: .tests
           snakefile: workflow/Snakefile
           args: "${{ matrix.rule }} --report report.zip"
 
       - name: Upload report
         uses: actions/upload-artifact@v3
-        if: matrix.technology == 'all' && matrix.rule != 'all -npr'
+        if: matrix.technology == 'all' && matrix.rule != 'all -np'
         with:
           name: report-rule-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}
           path: .tests/results/patient-reports/2022-01-01.zip
 
       - name: Upload logs
         uses: actions/upload-artifact@v3
-        if: matrix.technology == 'all' && matrix.rule != 'all -npr'
+        if: matrix.technology == 'all' && matrix.rule != 'all -np'
         with:
           name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}
           path: .tests/logs/
@@ -319,11 +319,11 @@ jobs:
         with:
           directory: .tests
           snakefile: workflow/Snakefile
-          args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
+          args: "-p --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"
 
       - name: Test report
         uses: snakemake/[email protected]
-        if: startsWith(matrix.rule, 'all -npr') != true
+        if: startsWith(matrix.rule, 'all -np') != true
         with:
           directory: .tests
           snakefile: workflow/Snakefile