From 652c19b67424f87571cd0e0b64e49ef1f52a3459 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Tue, 24 Jul 2018 13:15:21 +0200
Subject: [PATCH] Adapt Snakefile in response to changes in script for barplots
(utils/sv_consistency_barplot.R)
---
Snakefile | 10 ++++------
utils/sv_consistency_barplot.snakemake.R | 2 +-
2 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/Snakefile b/Snakefile
index 46859b7..03e704b 100644
--- a/Snakefile
+++ b/Snakefile
@@ -70,12 +70,12 @@ rule all:
bpdens = ["few","medium","many"],
method = METHODS),
expand("ploidy/{sample}/ploidy.{chrom}.txt", sample = SAMPLES, chrom = config["chromosomes"]),
- expand("sv_calls/{sample}/{window}_fixed_norm.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-{af}.pdf",
+ expand("sv_calls/{sample}/{window}_fixed_norm.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-{plottype}.pdf",
sample = SAMPLES,
window = [50000, 100000],
bpdens = ["few","medium","many"],
method = METHODS,
- af = ["high","med","low","rare"]),
+ plottype = ["byaf","bypos"]),
expand("haplotag/table/{sample}/full/haplotag-counts.{window}_fixed_norm.{bpdens}.tsv",
sample = SAMPLES,
window = [50000, 100000],
@@ -294,10 +294,8 @@ rule plot_SV_consistency_barplot:
input:
sv_calls = "sv_calls/{sample}/{windows}.{bpdens}/{method}.txt",
output:
- barplot_high = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-high.pdf",
- barplot_med = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-med.pdf",
- barplot_low = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-low.pdf",
- barplot_rare = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-rare.pdf",
+ barplot_bypos = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-bypos.pdf",
+ barplot_byaf = "sv_calls/{sample}/{windows}.{bpdens}/plots/sv_consistency/{method}.consistency-barplot-byaf.pdf",
log:
"log/plot_SV_consistency/{sample}/{windows}.{bpdens}.{method}.log"
script:
diff --git a/utils/sv_consistency_barplot.snakemake.R b/utils/sv_consistency_barplot.snakemake.R
index 351f1e8..c9a4fe8 100644
--- a/utils/sv_consistency_barplot.snakemake.R
+++ b/utils/sv_consistency_barplot.snakemake.R
@@ -4,4 +4,4 @@ sink(file=log, type='output')
source("utils/sv_consistency_barplot.R")
-SVplotting(snakemake@input[["sv_calls"]], snakemake@output[["barplot_high"]], snakemake@output[["barplot_med"]], snakemake@output[["barplot_low"]], snakemake@output[["barplot_rare"]])
+SVplotting(inputfile = snakemake@input[["sv_calls"]], outputfile.byPOS = snakemake@output[["barplot_bypos"]], outputfile.byVAF = snakemake@output[["barplot_byaf"]])
--
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