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 use beauris.workflows.drmaa.func_annot_orson

  • Set job_specs as follows in beauris.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.