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Infer conpair tumor-normal pairs from sample IDs #15

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Infer conpair tumor-normal pairs from sample IDs #15

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38 changes: 29 additions & 9 deletions workflow/rules/relatedness_test_day.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,12 @@ rule relatedness_all:
# Picard crosscheck (matrix + metrics)
"results/picard/crosscheck/metrics.txt",
"results/picard/crosscheck/matrix.txt",
# Conpair for declared tumor/normal pairs (optional – created only for pairs in expected list)
expand("results/conpair/{a}__{b}/concordance.tsv",
zip, a=[x["samples"][0] for x in config["expected"] if x["relationship"]=="tumor_normal"],
b=[x["samples"][1] for x in config["expected"] if x["relationship"]=="tumor_normal"]),
# Conpair for tumor/normal pairs detected from sample IDs
expand(
"results/conpair/{t}__{n}/concordance.tsv",
t=[p[0] for p in tn_pairs()],
n=[p[1] for p in tn_pairs()]
),
# Optional peddy
*( ["results/peddy/peddy.html"] if config.get("peddy", {}).get("enabled", False) else [] ),
# Final merged report
Expand Down Expand Up @@ -122,11 +124,27 @@ rule picard_crosscheck:
"""

#######################################################################
# CONPAIR (only for declared tumor_normal expected pairs)
# CONPAIR (for tumor/normal pairs inferred from sample IDs)
#######################################################################

def tn_pairs():
return [x["samples"] for x in config["expected"] if x["relationship"]=="tumor_normal"]
"""Identify tumor/normal pairs based on sample naming.

Samples ending with `_T` are assumed to be tumor and paired with a
corresponding sample ending with `_N` that shares the same prefix.
Only pairs for which both sample IDs exist and their associated files
are present on disk are returned.
"""
pairs = []
for s in SAMPLES:
if s.endswith("_T"):
n = f"{s[:-2]}_N"
if n in SAMPLES:
t_path, _ = sample_input(s)
n_path, _ = sample_input(n)
if os.path.exists(t_path) and os.path.exists(n_path):
pairs.append((s, n))
return pairs

rule conpair_mpileup:
input:
Expand Down Expand Up @@ -256,9 +274,11 @@ rule relatedness_report:
som_groups="results/somalier/cohort_groups.tsv",
picard_metrics="results/picard/crosscheck/metrics.txt",
picard_matrix="results/picard/crosscheck/matrix.txt",
conpair=expand("results/conpair/{a}__{b}/concordance.tsv",
zip, a=[x["samples"][0] for x in config["expected"] if x["relationship"]=="tumor_normal"],
b=[x["samples"][1] for x in config["expected"] if x["relationship"]=="tumor_normal"]),
conpair=expand(
"results/conpair/{t}__{n}/concordance.tsv",
t=[p[0] for p in tn_pairs()],
n=[p[1] for p in tn_pairs()]
),
output:
tsv="results/relatedness_qc/relatedness_summary.tsv",
html="results/relatedness_qc/relatedness_report.html"
Expand Down