From 0b64772634eb9fa08bc984537a629eb7b72cae62 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Thu, 27 Aug 2020 13:55:42 +1000
Subject: [PATCH] fixed missing quotation marks
---
dunnart/Snakefile | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/dunnart/Snakefile b/dunnart/Snakefile
index 816e9a9..cd994e1 100644
--- a/dunnart/Snakefile
+++ b/dunnart/Snakefile
@@ -56,6 +56,10 @@ rule all:
expand("results/bowtie2/{sample}_PPq30.sorted.dupmark.bam", sample=all_samples),
expand("results/bowtie2/{sample}_PPq30.sorted.dedup.bam", sample=all_samples),
expand("results/bowtie2/{sample}_PPq30.sorted.dedup.bai", sample=all_samples),
+ "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+ "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+ "logs/H3K4me3.mergeBAM",
+ "logs/H3K27ac.mergeBAM",
expand("results/qc/{sample}.unfiltered.flagstat.qc", sample=all_samples),
expand("results/qc/{sample}.dedup.flagstat.qc", sample=all_samples),
expand("results/qc/{sample}.dupmark.flagstat.qc", sample=all_samples),
@@ -191,8 +195,8 @@ rule indexBam:
rule mergeBAMreplicates:
input:
- H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam, results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"],
- H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam, results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"]
+ H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam", "results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"],
+ H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam", "results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"]
output:
H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam"
--
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