add option to specify assemblies via config file

README.md

@@ -80,6 +80,15 @@ snakemake -s /opt/software/ont-assembly-snake/Snakefile --use-conda --cores 20
 
 Assemblies created in each step are contained in the files `output.fa` in each folder and symlinked as `.fa` files in the `assemblies/` folder, see the example below.
 
+As an alternative to create subfolders within `assemblies/`, it is also possible to use a YAML file to list the desired assemblies, e.g. in a file called `samples.yaml`:
+```
+assemblies:
+  - mysample_flye+medaka
+  - mysample+filtlongMB500_flye+racon2+medaka
+  - mysample_raven2+medaka+pilon
+```
+and add the argument `--configfile samples.yaml` to the Snakemake command line.
+
 ## Test dataset
 A test dataset containing a pair of ONT and Illumina sequencing data from the same bacterial isolate is available in the repository [ont-assembly-snake-testdata](https://github.com/pmenzel/ont-assembly-snake-testdata). See the instructions therein on how to download the dataset and run the ont-assembly-snake and [score-assemblies](https://github.com/pmenzel/score-assemblies) workflows.
 

Snakefile

@@ -10,7 +10,7 @@ if config.get("run_score_assemblies", False):
     module score_assemblies:
         snakefile:
             github("pmenzel/score-assemblies", path="Snakefile", branch="master")
-            #"score-assemblies/Snakefile"
+            #  "score-assemblies/Snakefile"
         config:
             config
 
@@ -75,6 +75,10 @@ def get_R2_fq(wildcards):
 # ignore symlinks in assemblies/folder, e.g. sample_flye.fa -> assemblies/sample_flye/output.fa
 sample_assemblies = [a for a in sample_assemblies if not re.search("\.fa", a)]
 
+# if config files with list of assemblies is given, then use this instead of folders in assemblies/
+if config.get("assemblies", False):
+    sample_assemblies = list(set(config["assemblies"]))
+
 # if any desired assembly requires homopolish then at least one reference genome should be provided
 if not references and [
     string for string in sample_assemblies if "homopolish" in string