Merge pull request #210 from DendrouLab/fc_refmap

changes to accomodate different mem threads

CHANGELOG.md

@@ -10,9 +10,13 @@
 ### fixed
 
 - fixed error in `vis`
-    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
+  - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
+- fixed error in `refmap`
+  - high threads was not recognised, now fixed.
 
 ### dependencies
+- All the dependencies have been updated. 
+  - Python>=3.10 required
 
 ## v0.4.1
 

docs/release_notes.md

@@ -10,9 +10,13 @@
 ### fixed
 
 - fixed error in `vis`
-    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
+  - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
+- fixed error in `refmap`
+  - high threads was not recognised, now fixed.
 
 ### dependencies
+- All the dependencies have been updated. 
+  - Python>=3.10 required
 
 ## v0.4.1
 

panpipes/panpipes/pipeline_refmap.py

@@ -9,7 +9,7 @@
 from itertools import chain
 import glob
 
-# __file__="/well/cartography/users/zsj686/non_cart_projects/005-multimodal_scpipelines/src/sc_pipelines_muon_dev/panpipes/pipeline_refmap.py"
+
 PARAMS = P.get_parameters(
     ["%s/pipeline.yml" % os.path.splitext(__file__)[0],
      "pipeline.yml"])
@@ -104,7 +104,16 @@ def run_refmap_scvi(infile, outfile, log_file, ref_architecture ):
         cmd += " --predict_rf %(run_randomforest)s"
 
     cmd += " > %(log_file)s"
-    job_kwargs["job_threads"] = PARAMS['resources_threads_low']
+
+    if PARAMS['queues_gpu'] is not None:
+        job_kwargs["job_queue"] = PARAMS['queues_gpu']
+        job_kwargs["job_threads"] = int(PARAMS['resources_threads_gpu'])
+    elif PARAMS['queues_long'] is not None:
+            job_kwargs["job_queue"] = job_queue=PARAMS['queues_long']
+            job_kwargs["job_threads"] = int(PARAMS['resources_threads_high'])
+    else:
+        job_kwargs["job_threads"] = int(PARAMS['resources_threads_high'])
+
     P.run(cmd, **job_kwargs)
 
 
@@ -150,7 +159,7 @@ def run_scib_refmap(infile,logfile):
         if PARAMS['query_celltype'] is not None:
             cmd += " --covariate %(query_celltype)s"
     cmd += " > %(logfile)s"
-    job_kwargs["job_threads"] = PARAMS['resources_threads_medium']
+    job_kwargs["job_threads"] = PARAMS['resources_threads_high']
     P.run(cmd, **job_kwargs)  
 
 

panpipes/panpipes/pipeline_refmap/pipeline.yml

@@ -18,7 +18,7 @@ resources:
 condaenv:
 
 # allows for tweaking which queues jobs get submitted to, 
-# in case there is a special queue for long jobs or you have access to a gpu-sepcific queue
+# in case there is a special queue for long jobs or you have access to a gpu-specific queue
 # the default queue should be specified in your .cgat.yml file
 # leave as is if you do not want to use the alternative queues
 queues: