From 28fe501e4c23e30f1a667abd9b805c30ae7c12db Mon Sep 17 00:00:00 2001
From: fgypas <fgypas@gmail.com>
Date: Wed, 25 Aug 2021 09:37:57 +0200
Subject: [PATCH] Fix temp dir
---
workflow/Snakefile | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index f702c7e..2714fd7 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -705,7 +705,8 @@ rule sort_genomic_alignment_samtools:
current_rule + ".{seqmode}.stdout.log")
shell:
- "(samtools sort \
+ "(mkdir -p {output.prefix_temp_dir}; \
+ samtools sort \
-o {output.bam} \
-T {output.prefix_temp_dir} \
-@ {threads} \
@@ -725,13 +726,7 @@ rule index_genomic_alignment_samtools:
"samples",
"{sample}",
"map_genome",
- "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam"),
- prefix_temp_dir = os.path.join(
- config["output_dir"],
- "samples",
- "{sample}.{seqmode}",
- "sort_genomic_alignment_samtools"
- )
+ "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam")
output:
bai = os.path.join(
--
GitLab