updated GDB config files

config/GDB/config.yaml

@@ -79,9 +79,9 @@ fastqc:
 
 # List of assemblers for different read types
 assemblers:
-    sr: ["megahit", "metaspades"]
+    sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
     lr: ["flye"]
-    hy: ["metaspadeshybrid", "operams"]
+    hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
 
 # XXX
 flye:
@@ -105,12 +105,12 @@ operams:
 ##############################
 # Long-read assembly polishing
 
-# XXX
+# https://nanoporetech.github.io/medaka/index.html
 medaka:
     threads: 10 # do NOT set to large value (e.g. using 30 did not work)
     model: r941_min_high # the MinION model, high accuarcy
 
-# XXX
+# https://github.com/isovic/racon
 racon:
     threads: 30
 

config/GDB/sbatch.sh

 #!/bin/bash -l
 
-##############################
-# SLURM
-# NOTE: used for this script only, NOT for the snakemake call below
-
+# slurm settings if called using sbatch
 #SBATCH -J ONT_SMK
 #SBATCH -N 1
 #SBATCH -n 1
 #SBATCH -c 1
-#SBATCH --time=0-10:00:00
+#SBATCH --time=2-00:00:00
 #SBATCH -p batch
 #SBATCH --qos=qos-batch
 
-##############################
-# SNAKEMAKE
-
-# conda env name
+# conda env name or path
 ONTP_ENV="ONT_pilot"
-# number of cores for snakemake
-ONTP_CORES=60
-# snakemake file
-ONTP_SMK="workflow/Snakefile"
-# config file
-ONTP_CONFIG="config/GDB/config.yaml" # USER INPUT REQUIRED
-# slurm config file
+# number of concurrent jobs
+ONTP_JOBS=10
+# config files
+ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"
 # slurm cluster call
-ONTP_CLUSTER="-p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
-
-##############################
-# IMP
+ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
 
-# activate the env
 conda activate ${ONTP_ENV}
 
-# run the pipeline
-snakemake -s ${ONTP_SMK} -rp --cores ${ONTP_CORES} --configfile ${ONTP_CONFIG} \
---use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
---cluster-config ${ONTP_SLURM} --cluster "sbatch ${ONTP_CLUSTER}"
+snakemake -s workflow/Snakefile -rp --jobs ${ONTP_JOBS} --local-cores 1 \
+--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
+--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"

config/GDB/slurm.yaml

@@ -134,6 +134,22 @@ polishing_lr_medaka:
     n: 1
     explicit: ""
 
+mapping_bwa_mem_polishing_metat:
+    time: "00-02:00:00"
+    partition: "batch"
+    qos: "qos-batch"
+    nodes: 1
+    n: 1
+    explicit: ""
+
+polishing_metat_racon:
+    time: "00-04:00:00"
+    partition: "bigmem"
+    qos: "qos-bigmem"
+    nodes: 1
+    n: 1
+    explicit: ""
+
 # Annotation
 annotation_prodigal:
     time: "01-4:00:00"