updated GDB config files

config/GDB/config.yaml

@@ -2,7 +2,8 @@
 # STEPS
 
 # Steps to be done
-steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps: ["assembly", "mapping", "annotation", "analysis", "taxonomy"]
 steps_annotation: ["diamond", "rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case
 steps_analysis: ["quast", "cdhit", "mash_dist"]
 steps_taxonomy: ["kraken2", "kaiju"]
@@ -86,7 +87,7 @@ assemblers:
     # lr: ["flye"]
     # hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
     sr: ["megahit", "metaspades"]
-    lr: ["flye", "wtdbg2"]
+    lr: ["flye", "wtdbg2", "canu"]
     hy: ["metaspadeshybrid", "operams"]
 
 # https://github.com/fenderglass/Flye
@@ -100,6 +101,12 @@ wtdbg2:
     bin: "/scratch/users/sbusi/tools/wtdbg2/"
     genome_size: "1g"
 
+# https://canu.readthedocs.io/en/latest/
+canu:
+    threads: 24
+    # mem: "64g"
+    genome_size: "1g"
+
 # https://github.com/ablab/spades
 metaspades:
     threads: 10

config/GDB/sbatch.sh

@@ -5,14 +5,14 @@
 #SBATCH -N 1
 #SBATCH -n 1
 #SBATCH -c 1
-#SBATCH --time=2-00:00:00
+#SBATCH --time=3-00:00:00
 #SBATCH -p batch
 #SBATCH --qos=qos-batch
 
 # conda env name or path
 ONTP_ENV="ONT_pilot"
 # number of concurrent jobs
-ONTP_JOBS=30
+ONTP_JOBS=5
 # config files
 ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"

config/GDB/slurm.yaml

@@ -44,6 +44,14 @@ assembly_lr_wtdbg2:
     n: 1
     explicit: ""
 
+assembly_lr_canu:
+    time: "05-00:00:00"
+    partition: "bigmem"
+    qos: "qos-bigmem"
+    nodes: 1
+    n: 1
+    explicit: ""
+
 assembly_sr_megahit:
     time: "01-4:00:00"
     partition: "bigmem"