mondrian nextflow support

alhena_igo/cli.py

@@ -98,18 +98,33 @@ def clean(info: Info, analysis: str):
 @cli.command()
 @click.option('--analysis_id', help="MONDRIAN-HMMCOPY or SCDNA-ANNOTATION analysis primary key", required=True)
 @click.option('--project', 'projects', multiple=True, default=["DLP"], help="Projects to load analysis into")
-@click.option('--framework', type=click.Choice(['scp', 'mondrian']), help="Framework: scp or mondrian")
+@click.option('--framework', type=click.Choice(['scp', 'mondrian', 'mondrian_nf']), help="Framework: scp, mondrian or mondrian_nf (nextflow)")
 @click.option('--version', help="Isabl app version to load", required=True)
 @pass_info
 def load(info: Info, analysis_id: str, projects: List[str], framework: str, version: str):
     click.echo(f'Loading as ID {analysis_id}')
 
     if framework == 'scp':
         [alignment, hmmcopy, annotation] = alhena_igo.isabl.get_directories(analysis_id, framework, version)
-        data = load_qc_results(alignment, hmmcopy, annotation)
+        data = load_qc_results(
+            'scp', 
+            alignment_results_dir=alignment, 
+            hmmcopy_results_dir=hmmcopy,
+            annotation_results_dir=annotation
+        )
     elif framework == 'mondrian':
         [alignment, hmmcopy] = alhena_igo.isabl.get_directories(analysis_id, framework, version)
-        data = load_qc_results(alignment, hmmcopy)
+        data = load_qc_results(
+            'mondrian', 
+            alignment_results_dir=alignment, 
+            hmmcopy_results_dir=hmmcopy
+        )
+    elif framework == 'mondrian_nf':
+        [qc] = alhena_igo.isabl.get_directories(analysis_id, framework, version)
+        data = load_qc_results(
+            'mondrian_nf', 
+            qc_results_dir=qc
+        )
     else:
         raise Exception(f"Unknown framework option '{framework}'")
 

alhena_igo/isabl.py

@@ -61,8 +61,8 @@ def get_analysis_filtered_by_assembly(experiment_sys_id, app_name, assembly):
 
 def get_directories(analysis_pk: str, framework: str, version: str):
     """
-    Return QC results for Mondrian or SCP based off MONDRIAN-HMMCOPY or SCDNA-ANNOTATION
-    analysis primary key.
+    Return QC results for Mondrian (cromwell), Mondrain NF (nextflow) or SCP based off 
+    MONDRIAN-HMMCOPY, MONDRIAN-NF-QC or SCDNA-ANNOTATION analysis primary key.
     """
 
     if framework == 'mondrian':
@@ -79,6 +79,17 @@ def get_directories(analysis_pk: str, framework: str, version: str):
 
         return [alignment.storage_url, hmmcopy[0].storage_url]
 
+    elif framework == 'mondrian_nf':
+        qc = ii.get_analyses(
+            pk=analysis_pk, 
+            application__name='MONDRIAN-NF-QC',
+            status='SUCCEEDED',
+        )
+        assert len(qc) == 1
+
+        # quick way to add support mondrian-nf using exisiting mondrian logic
+        return [qc[0].storage_url]
+
     elif framework == 'scp':
         annotation = ii.get_analyses(pk=analysis_pk, application__name='SCDNA-ANNOTATION')
         assert len(annotation) == 1
@@ -139,6 +150,8 @@ def get_id(aliquot_id, framework, version):
 
     if framework == 'mondrian':
         app = 'MONDRIAN-HMMCOPY'
+    elif framework == 'mondrian-nf':
+        app = 'MONDRIAN-NF-QC'
     elif framework == 'scp':
         app = 'SCDNA-ANNOTATION'
     else:
@@ -163,6 +176,8 @@ def get_ids_from_isabl(project_pk, framework, version):
     app = ''
     if framework == 'mondrian':
         app = 'MONDRIAN-HMMCOPY'
+    elif framework == 'mondrian-nf':
+        app = 'MONDRIAN-NF-QC'
     elif framework == 'scp':
         app = 'SCDNA-ANNOTATION'
     else:

setup.py

@@ -49,7 +49,7 @@
     version=version,
     install_requires=[
         # Include dependencies here
-        "alhenaloader @ git+https://github.com/shahcompbio/alhenaloader.git@v1.0.6#egg=alhenaloader",
+        "alhenaloader @ git+https://github.com/shahcompbio/alhenaloader.git@v1.1.0#egg=alhenaloader",
         "isabl_cli @ git+https://github.com/papaemmelab/isabl_cli.git#egg=isabl_cli"
     ],
     entry_points="""