Commit ae3b5884 authored by Valentina Galata's avatar Valentina Galata
Browse files

updated GDB config files

parent 6690266a
......@@ -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
......
......@@ -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"
......
......@@ -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"
......
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