Merge branch 'master' into update-jinja2

# Conflicts:
#	poetry.lock

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 65.0.10
+current_version = 65.0.13
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "65.0.10"
+__version__ = "65.0.13"

cg/cli/workflow/base.py

@@ -14,6 +14,7 @@
 from cg.cli.workflow.mip_dna.base import mip_dna
 from cg.cli.workflow.mip_rna.base import mip_rna
 from cg.cli.workflow.mutant.base import mutant
+from cg.cli.workflow.nallo.base import nallo
 from cg.cli.workflow.raredisease.base import raredisease
 from cg.cli.workflow.rnafusion.base import rnafusion
 from cg.cli.workflow.taxprofiler.base import taxprofiler
@@ -27,16 +28,17 @@ def workflow():
 
 workflow.add_command(balsamic)
 workflow.add_command(balsamic_qc)
-workflow.add_command(balsamic_umi)
 workflow.add_command(balsamic_pon)
+workflow.add_command(balsamic_umi)
+workflow.add_command(fluffy)
+workflow.add_command(jasen)
 workflow.add_command(microsalt)
 workflow.add_command(mip_dna)
 workflow.add_command(mip_rna)
-workflow.add_command(fluffy)
-workflow.add_command(jasen)
 workflow.add_command(mutant)
+workflow.add_command(nallo)
 workflow.add_command(raredisease)
+workflow.add_command(raw_data)
 workflow.add_command(rnafusion)
 workflow.add_command(taxprofiler)
 workflow.add_command(tomte)
-workflow.add_command(raw_data)

cg/cli/workflow/nallo/__init__.py

@@ -0,0 +1 @@
+"""Init for module"""

cg/cli/workflow/nallo/base.py

@@ -0,0 +1,20 @@
+"""CLI support to create config and/or start NALLO."""
+
+import logging
+
+import rich_click as click
+
+from cg.cli.utils import CLICK_CONTEXT_SETTINGS
+from cg.constants.constants import MetaApis
+from cg.meta.workflow.analysis import AnalysisAPI
+from cg.meta.workflow.nallo import NalloAnalysisAPI
+
+LOG = logging.getLogger(__name__)
+
+
+@click.group(invoke_without_command=True, context_settings=CLICK_CONTEXT_SETTINGS)
+@click.pass_context
+def nallo(context: click.Context) -> None:
+    """GMS/Nallo analysis workflow."""
+    AnalysisAPI.get_help(context)
+    context.obj.meta_apis[MetaApis.ANALYSIS_API] = NalloAnalysisAPI(config=context.obj)

cg/meta/delivery_report/templates/macros/data_analysis/limitations.html

@@ -12,7 +12,7 @@ <h4 class="mt-4 mb-3">Teknisk beskrivning och begränsningar av analysen</h4>
     <tbody>
       {% for application in applications %}
       <tr>
-        <th scope="row">{{ application.tag }} (v{{ application.version }})</th>
+        <th scope="row">{{ application.tag }}</th>
         <td class="text-start">{{ application.description }}</td>
         <td class="text-start">{{ application.details }}</td>
         <td class="text-start">

cg/meta/delivery_report/templates/macros/order.html

@@ -31,7 +31,7 @@ <h3 class="mb-4">Beställning</h3>
             <td>{{ sample.name }} ({{ sample.id }})</td>
             <td>{{ sample.timestamps.ordered_at }}</td>
             <td>{{ sample.ticket }}</td>
-            <td>{{ sample.application.tag }} (v{{ sample.application.version }})</td>
+            <td>{{ sample.application.tag }}</td>
             <td>{% if customer_workflow != "taxprofiler" %} {{ sample.sex }} {% endif %}</td>
             <td>{{ sample.source }}</td>
             <!-- Sample status value -->

cg/meta/workflow/nallo.py

@@ -0,0 +1,20 @@
+"""Module for Nallo Analysis API."""
+
+import logging
+from cg.constants import Workflow
+from cg.meta.workflow.nf_analysis import NfAnalysisAPI
+from cg.models.cg_config import CGConfig
+
+LOG = logging.getLogger(__name__)
+
+
+class NalloAnalysisAPI(NfAnalysisAPI):
+    """Handles communication between Nallo processes
+    and the rest of CG infrastructure."""
+
+    def __init__(
+        self,
+        config: CGConfig,
+        workflow: Workflow = Workflow.NALLO,
+    ):
+        super().__init__(config=config, workflow=workflow)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "cg"
-version = "65.0.10"
+version = "65.0.13"
 description = "Clinical Genomics command center"
 readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"

tests/cli/workflow/nf_analysis/test_cli_workflow_base.py

@@ -10,7 +10,7 @@
 
 @pytest.mark.parametrize(
     "workflow",
-    NEXTFLOW_WORKFLOWS + [Workflow.JASEN],
+    NEXTFLOW_WORKFLOWS + [Workflow.JASEN] + [Workflow.NALLO],
 )
 def test_workflow_no_args(cli_runner: CliRunner, workflow: Workflow, request):
     """Test to see that workflow is added and prints help when no subcommand is specified."""

tests/conftest.py

@@ -44,6 +44,7 @@
 from cg.meta.tar.tar import TarAPI
 from cg.meta.transfer.external_data import ExternalDataAPI
 from cg.meta.workflow.jasen import JasenAnalysisAPI
+from cg.meta.workflow.nallo import NalloAnalysisAPI
 from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
 from cg.meta.workflow.taxprofiler import TaxprofilerAnalysisAPI
@@ -2481,6 +2482,16 @@ def sequencing_platform() -> str:
     return SequencingPlatform.ILLUMINA
 
 
+# Nallo fixtures
+@pytest.fixture(scope="function")
+def nallo_context(
+    cg_context: CGConfig,
+) -> CGConfig:
+    """Context to use in cli."""
+    cg_context.meta_apis["analysis_api"] = NalloAnalysisAPI(config=cg_context)
+    return cg_context
+
+
 # Raredisease fixtures
 @pytest.fixture(scope="function")
 def raredisease_dir(tmpdir_factory, apps_dir: Path) -> str: