BEAURIS modules
Several modules are implemented in BEAURIS, you can select the ones you’re interested in by configuring it in beauris.yml
TODO list all implemented modules
Functional annotation with the Nextflow pipeline Orson
The func_annot_orson
task runs:
busco
beedeem
diamond on uniref90
interproscan
eggnogmapper
Nextflow handles job submissions on SLURM (or other environments) and supervises the jobs.
Requirements
Requires singularity, nextflow, graphviz.
Download Orson code and singularity images (put them into orson/containers
)
git clone https://gitlab.ifremer.fr/bioinfo/workflows/orson.git
wget -r -nc -l1 -nH --cut-dirs=6 -A '*.sif' ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/sebimer/tools/ORSON/ -P orson/containers
Download the nextflow config file for your cluster, e.g.:
wget https://github.com/nf-core/configs/blob/master/conf/abims.config
You also need the uniref90 blast bank indexed with diamond and the BUSCO databases that can be downloaded at https://busco-data.ezlab.org/v5/data/ (see BUSCO user guide)
Usage
Set the CI step
func_annot
to usebeauris.workflows.drmaa.func_annot_orson
Set
job_specs
as follows inbeauris.yml
:
job_specs:
drmaa:
func_annot_orson:
# SCRATCH_WORK_DIR is supposed to be a scratch storage area for nextflow that can be cleaned up once the computation is completed.
env : >
source /etc/profile.d/modules.sh; module load nextflow/22.10.0 graphviz/2.40.1;
export ORSON_PATH=/path/to/orson/;
export BUSCO_DB_PATH=/path/to/busco/databases/
export BLAST_DB_PATH=/path/to/uniref90/diamond/uniref90_2022_03/uniref90.dmnd;
export CLUSTER_CONFIG_PATH=/path/to/cluster.config;
export SCRATCH_WORK_DIR=/path/to/scratch/workdir
Options
HECTAR (for heterokonts) is activated when it is defined as a task option in the yaml of the organism:
annotations:
- version: "OGS1.0"
[...]
task_options:
func_annot_orson:
hectar: true
Note: HECTAR can only be used on the ABIMS cluster for now because the source code is still not published.