Commit 4ee61449 authored by Valentina Galata's avatar Valentina Galata
Browse files

updated GDB config files

parent 7778266f
......@@ -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
......
#!/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}"
......@@ -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"
......
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