workflow update

workflows/example_configs/methods_config.yaml

@@ -7,15 +7,14 @@ seed: 2023
 
 # Methods to run for the pipeline, modify based on your need
 use_methods:
-  - "bass"
-#  - "BayesSpace"
+#  - "bass"
+  - "BayesSpace"
 #  - "DRSC"
 #  - "GraphST"
 #  - "SEDR"
 #  - "SOTIP"
-#  - "SpiceMix"
+#  - "SpiceMix"     # GPU access
 #  - "maple"
-#  - "meringue"
 #  - "precast"
 #  - "SC_MEB"
 #  - "spaGCN"
@@ -24,6 +23,7 @@ use_methods:
 #  - "STAGATE"       # res not n_clust
 #  - "scanpy"
 #  - "SpaceFlow"
-#  - "seurat"
+#  - "seurat"        # config 5 TODO
 #  - "BANKSY"
-#  - "SCAN-IT"       # buggy TODO
+#  - "SCAN-IT"       # buggy:data shape TODO
+#  - "meringue"      # buggy:no library found??? TODO

workflows/path_configs/methods.yaml

@@ -63,11 +63,11 @@ methods:
     script: method/precast/precast.r
     env_additional: method/precast/precast_env.sh
     optargs: method/precast/precast_optargs.json
-  SC.MEB:
-    env: method/SC.MEB/SC.MEB.yml
-    script: method/SC.MEB/SC.MEB.r
-    env_additional: method/SC.MEB/scmeb_env.sh
-    optargs: method/SC.MEB/SC.MEB_optargs.json
+  SC_MEB:
+    env: method/SC_MEB/SC_MEB.yml
+    script: method/SC_MEB/SC_MEB.r
+    env_additional: method/SC_MEB/scmeb_env.sh
+    optargs: method/SC_MEB/SC_MEB_optargs.json
   scanpy:
     env: method/scanpy/scanpy_env.yaml
     script: method/scanpy/method_scanpy.py
@@ -132,16 +132,16 @@ config_files:
     config_6: "config/config_6.json"
     config_7: "config/config_7.json"
     config_8: "config/config_8.json"
-    config_9: "config/config_9.json"
-    config_10: "config/config_10.json"
-    config_11: "config/config_11.json"
-    config_12: "config/config_12.json"
-    config_13: "config/config_13.json"
-    config_14: "config/config_14.json"
-    config_15: "config/config_15.json"
-    config_16: "config/config_16.json"
-    config_17: "config/config_17.json"
-    config_18: "config/config_18.json"
+#    config_9: "config/config_9.json"      # repetitive (res)
+#    config_10: "config/config_10.json"
+#    config_11: "config/config_11.json"
+#    config_12: "config/config_12.json"
+#    config_13: "config/config_13.json"
+#   config_14: "config/config_14.json"
+#    config_15: "config/config_15.json"
+#    config_16: "config/config_16.json"
+#    config_17: "config/config_17.json"
+#    config_18: "config/config_18.json"
   SpaceFlow:
     config_1: "config/config.json"
   SpiceMix:
@@ -179,14 +179,14 @@ config_files:
     config_1: "config/config_1.json"
     config_2: "config/config_2.json"
     config_3: "config/config_3.json"
-    config_4: "config/config_4.json"
-    config_5: "config/config_5.json"
+    #config_4: "config/config_4.json"     #decrepated
+    #config_5: "config/config_5.json"
   seurat:
     config_1: "config/config_1.json"
     config_2: "config/config_2.json"
     config_3: "config/config_3.json"
     config_4: "config/config_4.json"
-    config_5: "config/config_5.json"
+#    config_5: "config/config_5.json"     # buggy
   stardust:
     config_1: "config/config_1.json"
     config_2: "config/config_2.json"

workflows/readme.md

@@ -0,0 +1,14 @@
+## Workflow modification
+
+* git_dir and data_dir/result_dir in every config file
+
+## How to run snakemake
+
+Running snakemake: download -> preprocessing -> methods -> metrics
+
+* dry run: `snakemake -s <process>.smk -nf`
+
+* actual run `snakemake -s <process>.smk --cores <n_of_cores> --use-conda --ri`
+     * `ri`: in case you use keyboard interruption to quit the previous job. This will make sure snakemake rereun those incomplete job.
+
+* Try not to kill snakemake when it's installing conda packages.