Moved splitting to scripts directive

Author: maurerv

workflow/Snakefile

@@ -156,14 +156,8 @@ checkpoint cluster_sequence_length:
        "docker://kosinskilab/fold:latest",
     conda:
         "envs/alphapulldown.yaml",
-    shell:"""
-        python3 workflow/scripts/cluster_sequence_length.py \
-            --folds {params.folds} \
-            --output_file {output} \
-            --protein_delimiter {params.protein_delimiter} \
-            --bin_size {params.cluster_bin_size} \
-            --features_directory {params.feature_directory}
-        """
+    script:
+        "scripts/cluster_sequence_length.py"
 
 def lookup_features(wildcards):
     if config.get("cluster_jobs", False):

workflow/scripts/cluster_sequence_length.py

@@ -35,14 +35,14 @@ def parse_args():
         dest="features_directory",
         type=str,
         nargs="+",
-        required=True,
+        required=False,
         help="Path to computed monomer features.",
     )
     parser.add_argument(
         "--bin_size",
         dest="bin_size",
         type=int,
-        required=True,
+        required=False,
         default=150,
         help="Bin size used for clustering sequences.",
     )
@@ -55,6 +55,19 @@ def parse_args():
         help="Path to comma separated output file.",
     )
     args = parser.parse_args()
+
+    try:
+        args.folds = snakemake.params.folds
+        args.output_file = snakemake.output[0]
+        args.protein_delimiter = snakemake.params.protein_delimiter
+        args.bin_size = snakemake.params.cluster_bin_size
+        args.features_directory = [snakemake.params.feature_directory, ]
+    except Exception:
+        pass
+
+    if args.folds is None:
+        raise ValueError("--folds needs to be specified.")
+
     return args