updated GDB config files

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

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
 

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"