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Commit c29b603c authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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aggregates somalier only for input samples- #6

parent a1684120
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1 merge request!2QC under one umbrella (well mostly) under QuaC
......@@ -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
"""
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