From 689e112bf859ec1248a080105c10385d0b01a724 Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Mon, 3 Aug 2020 07:54:28 +0200
Subject: [PATCH] updated GDB config files
---
config/GDB/config.yaml | 8 +++++++-
config/GDB/sbatch.sh | 2 +-
config/GDB/slurm.yaml | 8 ++++++++
3 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/config/GDB/config.yaml b/config/GDB/config.yaml
index 40e9db0..e4166f3 100644
--- a/config/GDB/config.yaml
+++ b/config/GDB/config.yaml
@@ -86,7 +86,7 @@ assemblers:
# lr: ["flye"]
# hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
sr: ["megahit", "metaspades"]
- lr: ["flye"]
+ lr: ["flye", "wtdbg2"]
hy: ["metaspadeshybrid", "operams"]
# https://github.com/fenderglass/Flye
@@ -94,6 +94,12 @@ flye:
threads: 10
genome_size: "1g"
+# https://github.com/ruanjue/wtdbg2
+wtdbg2:
+ threads: 10
+ bin: "/scratch/users/sbusi/tools/wtdbg2/"
+ genome_size: "1g"
+
# https://github.com/ablab/spades
metaspades:
threads: 10
diff --git a/config/GDB/sbatch.sh b/config/GDB/sbatch.sh
index 77ae56e..174e0ad 100755
--- a/config/GDB/sbatch.sh
+++ b/config/GDB/sbatch.sh
@@ -5,7 +5,7 @@
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 1
-#SBATCH --time=0-06:00:00
+#SBATCH --time=2-00:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
diff --git a/config/GDB/slurm.yaml b/config/GDB/slurm.yaml
index 979dfaa..a793c4f 100644
--- a/config/GDB/slurm.yaml
+++ b/config/GDB/slurm.yaml
@@ -36,6 +36,14 @@ assembly_lr_flye:
n: 1
explicit: ""
+assembly_lr_wtdbg2:
+ time: "00-8:00:00"
+ partition: "bigmem"
+ qos: "qos-bigmem"
+ nodes: 1
+ n: 1
+ explicit: ""
+
assembly_sr_megahit:
time: "01-4:00:00"
partition: "bigmem"
--
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