number log files

panpipes/panpipes/pipeline_deconvolution_spatial.py

@@ -45,7 +45,7 @@ def run_cell2location(input_spatial, outfile_spatial, sample_prefix, input_singl
 
     figdir = "./figures/Cell2Location/" + sample_prefix
     output_dir = "./cell2location.output/" + sample_prefix
-    log_file = "Cell2Location_" + sample_prefix + ".log"
+    log_file = "1_Cell2Location_" + sample_prefix + ".log"
     cmd = """
         python %(py_path)s/run_cell2location.py
         --input_spatial %(input_spatial)s
@@ -114,7 +114,7 @@ def run_tangram(input_spatial, outfile_spatial, sample_prefix, input_singlecell)
 
     figdir = "./figures/Tangram/" + sample_prefix
     output_dir = "./tangram.output/" + sample_prefix
-    log_file = "Tangram_" + sample_prefix + ".log"
+    log_file = "2_Tangram_" + sample_prefix + ".log"
     cmd = """
         python %(py_path)s/run_tangram.py
         --input_spatial %(input_spatial)s

panpipes/panpipes/pipeline_preprocess_spatial.py

@@ -54,7 +54,7 @@ def gen_filter_jobs():
 def filter_mudata(infile_path,outfile):
     print('processing file = %s' % str(infile_path))
     log_file = os.path.basename(outfile)
-    log_file= "filtering."+log_file.replace("filtered.h5mu","") + ".log"
+    log_file= "1_filtering."+log_file.replace("filtered.h5mu","") + ".log"
 
 
     filter_dict = dictionary_stripper(PARAMS['filtering'])
@@ -83,7 +83,7 @@ def run_plotqc_query(pqc_dict):
 @active_if(PARAMS['filtering_run'])
 @transform(filter_mudata,
            regex("./filtered.data/(.*)_filtered.h5(.*)"), 
-           r"./logs/postfilterplot.\1.log")
+           r"./logs/2_postfilterplot.\1.log")
 def postfilterplot_spatial(filt_file,log_file):
     print(filt_file)    
     print(log_file)
@@ -105,7 +105,7 @@ def postfilterplot_spatial(filt_file,log_file):
 
 @transform(filter_mudata,
            regex("./filtered.data/(.*)_filtered.h5(.*)"), 
-           r"./logs/preprocess.\1.log")
+           r"./logs/3_preprocess.\1.log")
 def spatial_preprocess(filt_file,log_file):
     if os.path.exists("figures/spatial") is False:
         os.mkdir("figures/spatial")

panpipes/panpipes/pipeline_qc_spatial.py

@@ -108,7 +108,7 @@ def load_mudatas(spatial_path, outfile,
         --spatial_metadata %(spatial_metadata)s 
         --spatial_transformation %(spatial_transformation)s
         """
-    cmd += " > logs/make_mudatas_%(sample_id)s.log"
+    cmd += " > logs/1_make_mudatas_%(sample_id)s.log"
     print(cmd)
     job_kwargs["job_threads"] = PARAMS['resources_threads_medium']
     P.run(cmd, **job_kwargs)
@@ -121,7 +121,7 @@ def load_mudatas(spatial_path, outfile,
 @follows(mkdir("./figures"))
 @transform(load_mudatas,
            regex("./tmp/(.*)_raw.h5(.*)"), 
-           r"./logs/spatialQC_\1.log")
+           r"./logs/2_spatialQC_\1.log")
 def spatialQC(infile,log_file):
     spatial_filetype = assays[infile]
     resources_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), "resources")
@@ -168,7 +168,7 @@ def run_plotqc_query(pqc_dict):
 @active_if(run_plotqc_query(PARAMS['plotqc']))
 @transform(load_mudatas, 
            regex("./tmp/(.*)_raw.h5(.*)"),
-           r"./logs/qcplot.\1.log")
+           r"./logs/3_qcplot.\1.log")
 def plotQC_spatial(unfilt_file,log_file):
     spatial_filetype = assays[unfilt_file]
     unfilt_file = unfilt_file.replace("_raw","_unfilt")