Fix --no-json container run flag error issue

.github/workflows/PyTest.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up PDM
-      uses: pdm-project/setup-pdm@v4.1
+      uses: pdm-project/setup-pdm@v4
       with:
         python-version: '3.x'
 

.github/workflows/Sync-dev-with-main.yml

@@ -13,7 +13,7 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' || github.event_name == 'workflow_dispatch' }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

.github/workflows/Tag-and-Release.yml

@@ -19,15 +19,15 @@ jobs:
     if: startsWith(github.event.pull_request.title, 'Release:') && github.event.pull_request.merged == true
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: Setup Git
         run: |
           git config --local user.email "github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"
       - name: Setup PDM
-        uses: pdm-project/setup-pdm@v4.1
+        uses: pdm-project/setup-pdm@v4
         with:
           python-version: '3.x'
       - name: Get tag

.github/workflows/Update-Version-and-create-Realeases-PR.yml

@@ -28,7 +28,7 @@ jobs:
             exit 1
           fi
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
           ref: main
@@ -41,7 +41,7 @@ jobs:
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git config user.name "github-actions[bot]"
       - name: Setup PDM
-        uses: pdm-project/setup-pdm@v4.1
+        uses: pdm-project/setup-pdm@v4
         with:
           python-version: '3.x'
       - name: Setup GenPipes

genpipes/core/utils.py

@@ -114,9 +114,6 @@ def container_wrapper_argparse(script, argv):
 
         wrap_option = ['--container', 'wrapper', parsed.wrap]
 
-        if ('batch' in argv) and '--no-json' not in argv:
-            parser.error('Combining --wrap  and -j "batch" options requires --no-json')
-
         sys.stderr.write('wrapping\n')
         sys.stderr.write(f"{parsed.wrap} {script} {' '.join(argv)} {' '.join(wrap_option)}\n")
         # Running the pipeline inside the container

genpipes/pipelines/common.py

@@ -31,6 +31,7 @@
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(sys.argv[0]))))
 
 # GenPipes Modules
+from ..__version__ import __version__
 from ..core.config import global_conf, _raise, SanitycheckError
 from ..core.job import Job, concat_jobs, pipe_jobs
 from ..core.pipeline import Pipeline
@@ -147,13 +148,18 @@ def genpipes_log(self):
         readset_files = ",".join(list_name.values())
         unique_identifier = f"{server_ip}-{pipeline_name}-{readset_files}".replace("'", "''")
 
-        request = '&'.join([
+        request_parts = [
             "hostname=" + host_name,
             "ip=" + server_ip,
             "pipeline=" + pipeline_name,
             "steps=" + ",".join([step.name for step in self.step_to_execute]),
-            "samples=" + str(len(self.samples))
-        ])
+            "samples=" + str(len(self.samples)),
+            "version=" + __version__,
+            "user=" + (os.environ.get("USER") or os.getlogin()),
+        ]
+        if self.protocol:
+            request_parts.append("protocol=" + self.protocol)
+        request = '&'.join(request_parts)
         # that is crazy, to have to rely on the bash interface/arguments that deep in the code.
         self.job_scheduler.write("""
 {separator_line}