From 2c544b0a0f16e569ecbf4b312962b739a810ef5c Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 9 Dec 2019 11:11:45 +0100
Subject: [PATCH] Trying to relax memory limitations.
Pisa has more memory. Trim and dedup seems to be a bottleneck.
---
libworkflows | 2 +-
small_RNA-seq/small_RNA-seq.snakefile | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/libworkflows b/libworkflows
index 3230409..a6a8d82 160000
--- a/libworkflows
+++ b/libworkflows
@@ -1 +1 @@
-Subproject commit 3230409c45b98f697f50153d76845f1514fbdabc
+Subproject commit a6a8d82cdea5cfb481637fb65e0441d615111b59
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index f990ba0..f287f44 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -898,8 +898,8 @@ rule trim_and_dedup:
nb_trimmed = OPJ(data_dir, "trimmed", "{lib}_{rep}_nb_trimmed.txt"),
nb_deduped = OPJ(data_dir, "trimmed", "{lib}_{rep}_nb_deduped.txt"),
threads: 2
- resources:
- mem_mb=1049300
+ #resources:
+ # mem_mb=1049300
message:
"Trimming adaptor from raw data, deduplicating reads, removing random 5' {trim5}-mers and 3' {trim3}-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
--
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