add option for running score-assemblies

README.md

@@ -275,7 +275,7 @@ snakemake -s /opt/software/ont-assembly-snake/Snakefile --use-conda --cores 20 -
 
 Snakemake will recursively handle the dependencies for each assembly,
 and create folders for all intermediate steps automatically.
-Additionally, a symlink is created for each output assembly in the `assemblies/` folder, so they can easily be used as input for [score-assemblies](https://github.com/pmenzel/score-assemblies).
+Additionally, a symlink is created for each output assembly in the `assemblies/` folder.
 
 For the above example, the folders will look like this after running the workflow:
 ```
@@ -319,5 +319,10 @@ For the above example, the folders will look like this after running the workflo
 ```
 (Not shown is the content of each subfolder in `assemblies/` and some auxiliary files.)
 
+## score-assemblies
+
+The assemblies generated by this workflow can be evaluated using the [score-assemblies](https://github.com/pmenzel/score-assemblies) workflow.
+One can either download the score-assemblies repository separately and just run it in the same folder after ont-assembly-snake is done, see the [README](https://github.com/pmenzel/score-assemblies/blob/master/README.md) or
+add the Snakemake command line parameter `--config run_score_assemblies=1` to the Snakemake call of ont-assembly-snake.
 
 

Snakefile

@@ -1,20 +1,29 @@
 from glob import glob
 import pandas as pd
 
-shell.executable("/bin/bash")
+from snakemake.utils import min_version
+
+min_version("6.0")
+
+if config.get("run_score_assemblies", False):
+
+    module score_assemblies:
+        snakefile:
+            github("pmenzel/score-assemblies", path="Snakefile", branch="master")
+            #"score-assemblies/Snakefile"
+        config:
+            config
+
+    use rule * from score_assemblies as score_assemblies_*
+
+    ruleorder: proovframe_diamond_index > score_assemblies_diamond_ref_makedb
 
 
 filtlong_min_read_length = "1000"
 if config.get("filtlong_min_read_length", False):
     filtlong_min_read_length = config["filtlong_min_read_length"]
 print("filtlong min. read length = " + str(filtlong_min_read_length))
 
-# not needed anymore in flye 2.8
-# genome_size = "6m"
-# if config.get('genome_size',False):
-#  genome_size = config['genome_size']
-# print("genome size = " + genome_size)
-
 medaka_model = None
 if config.get("medaka_model", False):
     medaka_model = config["medaka_model"]