From 3c4c90f4aa2ace24301ca527a7f1f022402c8706 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 26 Feb 2018 16:38:15 +0100
Subject: [PATCH] mark tmp dir as ancient for markdup
---
Snakefile | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/Snakefile b/Snakefile
index b7ce2cb..8e80717 100644
--- a/Snakefile
+++ b/Snakefile
@@ -76,13 +76,6 @@ CHUNKS = split_genome(REFERENCE)
def out_path(path):
return join(OUT_DIR, path)
-
-try:
- mkdir(out_path("tmp"))
-except OSError:
- pass
-
-
def get_r(strand, wildcards):
"""Get fastq files on a single strand for a sample"""
s = SAMPLE_CONFIG['samples'].get(wildcards.sample)
@@ -221,13 +214,12 @@ rule markdup:
"""Mark duplicates in BAM file"""
input:
bam = out_path("{sample}/bams/{sample}.sorted.bam"),
- params:
- tmp = out_path("tmp")
+ tmp = ancient(out_path("tmp"))
output:
bam = out_path("{sample}/bams/{sample}.markdup.bam"),
metrics = out_path("{sample}/bams/{sample}.markdup.metrics")
conda: "envs/picard.yml"
- shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={params.tmp} " \
+ shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} " \
"INPUT={input.bam} OUTPUT={output.bam} " \
"METRICS_FILE={output.metrics} " \
"MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=500"
--
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