Provide the list of samples to weighted distances script

PathoGenOmics-Lab · Sep 13, 2023 · d17d1fb · d17d1fb
1 parent 6a48dd5
commit d17d1fb
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diff --git a/workflow/rules/distances.smk b/workflow/rules/distances.smk
@@ -2,6 +2,7 @@ rule weighted_distances:
     threads: 4
     conda: "../envs/biopython.yaml"
     params:
+        samples = expand("{sample}", sample = iter_samples()),
         mask_class = ["mask"],
         tsv_reference = OUTDIR/f"{OUTPUT_NAME}.ancestor.fasta",
         reference = OUTDIR/"reference.fasta"

diff --git a/workflow/scripts/weighted_distances.py b/workflow/scripts/weighted_distances.py
@@ -159,7 +159,8 @@ def main():
 
     logging.info("Reading input tables")
     df = read_and_concatenate_tsvs(snakemake.input.tsv, reference, outgroup, outgroup_name)
-    cov_list = df["REGION"].unique().tolist()
+    cov_list = snakemake.params.samples
+    cov_list.append(outgroup_name)
 
     logging.info(f"Parallelizing the calculation with {snakemake.threads} jobs")
     freq = create_freq_dict(snakemake.input.tsv)