Commit 1648784c authored by Valentina Galata's avatar Valentina Galata
Browse files

zymo: config: updated rumen (to match bright_future branch); rm unused zymo configs

parent 932628f9
......@@ -3,7 +3,7 @@
# Steps to be done
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps: ["preprocessing", "assembly"]
steps: ["preprocessing", "assembly", "mapping"]
steps_annotation: ["rgi", "plasflow", "minced", "barrnap", "kegg"] # prodigal is run in any case
steps_analysis: ["quast", "mash", "mashmap", "fastani", "mummer", "cdhit", "diamond", "cov"]
steps_taxonomy: ["kraken2", "kaiju"]
......
......@@ -20,6 +20,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 5 --local-cores 1 \
snakemake -s workflow/Snakefile -rp --jobs 5 --local-cores 1 --rerun-incomplete \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
......@@ -78,15 +78,15 @@ mapping_bwa_idx_asm:
partition: "batch"
mapping_bwa_mem_asm_sr:
time: "00-00:30:00"
time: "00-02:00:00"
partition: "batch"
mapping_bwa_mem_asm_lr:
time: "00-04:00:00"
time: "00-08:00:00"
partition: "batch"
mapping_bwa_mem_asm_hy:
time: "00-01:00:00"
time: "00-02:00:00"
partition: "batch"
# Annotation
......
# Main requirements
work_dir: "/scratch/users/sbusi/zymo"
results_dir: "/scratch/users/sbusi/zymo/results"
data_dir: "/scratch/users/sbusi/zymo/Zymo/results"
ref_genomes_dir: "/scratch/users/sbusi/zymo/results/data_ref_genomes"
# Assembly
# List of assemblers for different read types: assembler names MUST be UNIQUE
assemblers:
sr: ["megahit", "metaspades"]
lr: ["flye", "canu"]
# hy: ["metaspadeshybrid", "operamsmegahit", "operamsmetaspades"]
hy: ["metaspadeshybrid"]
# Zymo reference genomes
ref_genomes:
bsubtilis: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/bsubtilis_pb.fasta"
efaecalis: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/efaecalis_pb.fasta"
ecoli: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/ecoli_pb.fasta"
lmonocytogenes: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/lmonocytogenes_pb.fasta"
paeruginosa: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/paeruginosa_pb.fasta"
scerevisiae: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/scerevisiae_pb.fasta"
senterica: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/senterica_pb.fasta"
saureus: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/saureus_pb.fasta"
lfermentum: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/lfermentum_ontlumina.fasta"
cneoformans: "https://github.com/al-mcintyre/mCaller_analysis_scripts/raw/master/assemblies/cneoformans_ont.fasta"
# Additional params
# single_fast5_dir: "data_single_fast5"
# multi_fast5_dir: "data_multi_fast5"
# Annotation tools
prodigal:
threads: 12
diamond:
threads: 20
# Comparison tools
sibeliaz:
threads: 24
kmer: 25
mem: 2
#!/bin/bash -l
##############################
# SLURM
# NOTE: used for this script only, NOT for the snakemake call below
#SBATCH -J ONT_SMK
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 1
#SBATCH --time=2-00:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
#SBATCH --mail-type=end,fail
#SBATCH --mail-user=valentina.galata@uni.lu
##############################
# SNAKEMAKE
# conda env name
ONTP_ENV="snakemake"
# number of cores for snakemake
ONTP_CORES=20
# snakemake file
ONTP_SMK="workflow_zymo/Snakefile"
# config file
ONTP_CONFIG="config/zymo/config.zymo.yaml"
# slurm config file
ONTP_SLURM="config/zymo/slurm.zymo.yaml"
# slurm cluster call
ONTP_CLUSTER="{cluster.call} -t {cluster.runtime} -n {cluster.threads} -p {cluster.partition} -N {cluster.nodes} -q {cluster.quality} --job-name={cluster.job-name}"
##############################
# Snakemake
# activate the env
conda activate ${ONTP_ENV}
# unlock the pipeline
snakemake -s ${ONTP_SMK} -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}" --unlock
# run the pipeline
snakemake -s ${ONTP_SMK} -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"
__default__:
call: "sbatch"
nodes: 1
partition: "batch"
quality: "normal"
runtime: "0-00:10:00"
threads: 1
job-name: "ZYMO_REF.{rule}"
zymo_download:
partition: "batch"
quality: "normal"
runtime: "0-00:15:00"
zymo_concat:
partition: "batch"
quality: "normal"
runtime: "0-00:10:00"
zymo_prodigal:
partition: "batch"
qos: "normal"
runtime: "00-00:30:00"
diamond_db:
partition: "batch"
quality: "normal"
runtime: "00-00:15:00"
analysis_diamond:
partition: "batch"
quality: "normal"
runtime: "00-00:15:00"
get_headers:
runtime: "00-00:05:00"
zymo_headers:
runtime: "00-00:05:00"
comparison:
runtime: "00-00:15:00"
sibeliaz:
partition: "batch"
quality: "normal"
runtime: "00-00:30:00"
zymo_sibeliaz:
partition: "batch"
quality: "normal"
runtime: "00-00:30:00"
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