From 22407cc46b54e361843c3ddfc88fdb0a49cd9d8f Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Sat, 27 Oct 2018 17:41:24 +0200
Subject: [PATCH] remove cell-mixing experiment
---
Snakefile | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/Snakefile b/Snakefile
index 8b6e3d6..a3f4ad7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -67,7 +67,7 @@ BPDENS = [
"selected_j{}_s{}_scedist{}".format(joint, single, scedist) for joint in [0.1] for single in [0.5] for scedist in [5,20]
]
-singularity: "docker://smei/mosaicatcher-pipeline:v0.1"
+singularity: "docker://smei/mosaicatcher-pipeline:latest"
localrules:
all,
@@ -1083,14 +1083,14 @@ rule aggregate_summary_statistics:
shell:
"(head -n1 {input.tsv[0]} && (tail -n1 -q {input.tsv} | sort -k1) ) > {output}"
-rule evaluate_cell_mixing:
- input:
- sv_calls = expand('sv_calls/{sample}/{{windows}}.{{bpdens}}/{{method}}.txt', sample=SAMPLES),
- truth = '../input-data/ground_truth/RPE-BM510_manual/clonal-events.tsv',
- output:
- tsv = 'cell-mixing-eval/{windows}.{bpdens}/{method}.tsv'
- log:
- 'cell-mixing-eval/{windows}.{bpdens}/{method}.log'
- run:
- names = ','.join(SAMPLES)
- shell('utils/evaluate_cell_mixing.py --names {names} {input.truth} {input.sv_calls} > {output.tsv} 2> {log}')
+#rule evaluate_cell_mixing:
+# input:
+# sv_calls = expand('sv_calls/{sample}/{{windows}}.{{bpdens}}/{{method}}.txt', sample=SAMPLES),
+# truth = config["ground_truth_clonal"][wildcards.sample],
+# output:
+# tsv = 'cell-mixing-eval/{sample}/{windows}.{bpdens}/{method}.tsv'
+# log:
+# 'cell-mixing-eval/{sample}/{windows}.{bpdens}/{method}.log'
+# run:
+# names = ','.join(SAMPLES)
+# shell('utils/evaluate_cell_mixing.py --names {names} {input.truth} {input.sv_calls} > {output.tsv} 2> {log}')
--
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