pin snakemake <=6.7.0 in CI

Author: cokelaer

.github/workflows/main.yml

@@ -50,6 +50,7 @@ jobs:
       run: |
          pip install .
          pip install multiqc
+         pip install "snakemake<=6.7.0"
 
     - name: testing
       run: |

sequana_pipelines/mapper/main.py

@@ -65,6 +65,10 @@ def __init__(self, prog=NAME, epilog=None):
         pipeline_group.add_argument("--create-bigwig", action="store_true",
             help="create the bigwig files from the BAM files" )
 
+        self.add_argument("--run", default=False, action="store_true",
+            help="execute the pipeline directly")
+
+
     def parse_args(self, *args):
         args_list = list(*args)
         if "--from-project" in args_list: