aggregates somalier only for input samples- #6

workflow/rules/relatedness_ancestry.smk

@@ -41,7 +41,7 @@ rule somalier_relate:
         log=OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.log",
     params:
         outdir=lambda wildcards, output: Path(output["out"][0]).parent,
-        indir=lambda wildcards, input: Path(input[0]).parent,
+        infiles=lambda wildcards: str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / f"{{{','.join(SAMPLES)}}}.somalier")
     shell:
         r"""
         echo "Heads up: Somalier is run on all samples in the input directory; Not just the files mentioned in the rule's input."
@@ -50,7 +50,7 @@ rule somalier_relate:
             --ped {input.ped} \
             --infer \
             --output-prefix {params.outdir}/somalier \
-            {params.indir}/*.somalier \
+            {params.infiles} \
             > {log} 2>&1
         """
 
@@ -73,15 +73,13 @@ rule somalier_ancestry:
         log=OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.log",
     params:
         outdir=lambda wildcards, output: Path(output["out"][0]).parent,
-        indir=lambda wildcards, input: Path(input[0]).parent,
+        infiles=lambda wildcards: str(OUT_DIR / "project_level_qc" / "somalier" / "extract" / f"{{{','.join(SAMPLES)}}}.somalier")
     shell:
         r"""
-        echo "Heads up: Somalier is run on all samples in the input directory; Not just the files mentioned in the rule's input."
-
         somalier ancestry \
             --output-prefix {params.outdir}/somalier \
             --labels {input.labels_1kg} \
             {input.somalier_1kg}/*.somalier ++ \
-            {params.indir}/*.somalier \
+            {params.infiles} \
             > {log} 2>&1
         """