updated GDB contig files

config/GDB/config.yaml

@@ -3,6 +3,8 @@
 
 # Pipeline steps to be done: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
 steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
+steps_annotation: ["diamond", "rgi", "plasflow", "minced"] # prodigal is run in any case
+steps_analysis: ["quast", "cdhit", "mash_dist"]
 
 ############################################################
 # INPUT
@@ -77,11 +79,14 @@ fastqc:
 ##############################
 # Assembly
 
-# List of assemblers for different read types
+# List of assemblers for different read types: assembler names MUST be UNIQUE
 assemblers:
-    sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
+    # sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
+    # lr: ["flye"]
+    # hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
+    sr: ["megahit", "metaspades"]
     lr: ["flye"]
-    hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
+    hy: ["metaspadeshybrid", "operams"]
 
 # https://github.com/fenderglass/Flye
 flye:

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=1-00:00:00
 #SBATCH -p batch
 #SBATCH --qos=qos-batch
 
 # conda env name or path
 ONTP_ENV="ONT_pilot"
 # number of concurrent jobs
-ONTP_JOBS=10
+ONTP_JOBS=20
 # config files
 ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"

config/GDB/slurm.yaml

@@ -152,7 +152,7 @@ polishing_metat_racon:
 
 # Annotation
 annotation_prodigal:
-    time: "01-4:00:00"
+    time: "00-2:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1