GDB config: sormerna cores and runtime, other minor changes

config/GDB/config.yaml

@@ -74,7 +74,7 @@ fastp:
 
 # rRNA gene filtering
 sortmerna:
-    threads: 30
+    threads: 20
     # References to be used (w/ md5sums)
     refs: [
         # db6e72022cf650c4b33bd888b92a0391  silva-bac-16s-id90.fasta
@@ -95,7 +95,7 @@ fastqc:
 # List of assemblers for different read types: assembler names MUST be UNIQUE
 assemblers:
     sr: ["megahit", "metaspades"]
-    lr: ["flye", "wtdbg2"]
+    lr: ["flye", "wtdbg2", "canu"]
     hy: ["metaspadeshybrid", "operams"]
     hyhy: []
 

config/GDB/sbatch.sh

@@ -11,8 +11,6 @@
 
 # conda env name or path
 ONTP_ENV="ONT_pilot"
-# number of concurrent jobs
-ONTP_JOBS=10
 # config files
 ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"
@@ -21,6 +19,6 @@ ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit}
 
 conda activate ${ONTP_ENV}
 
-snakemake -s workflow/Snakefile -rp --jobs ${ONTP_JOBS} --local-cores 1 \
+snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
 --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
 --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"

config/GDB/slurm.yaml

@@ -28,7 +28,7 @@ fastp_sr:
     explicit: ""
 
 sortmerna_filt:
-    time: "01-00:00:00"
+    time: "01-12:00:00"
     partition: "batch"
     qos: "qos-batch"
     nodes: 1