example_job_def_mn5.job

#!/bin/bash

#SBATCH --job-name=metaline_singu_testy # Job’s name (to trace in)
#SBATCH --output=/gpfs/projects/bsc40/current/dmajer/metaline-testy-output/err_out/jobnm_%j.out # Output file, where
#SBATCH --error=/gpfs/projects/bsc40/current/dmajer/metaline-testy-output/err_out/jobnm_%j.err # File where the error is written

#SBATCH --ntasks=1 # The number of parallel tasks
#SBATCH --cpus-per-task=24 # Number of CPUs per run task
#SBATCH --tasks-per-node=1 # The number of allocated task/node

#SBATCH --qos=gp_bscls # The queue for the job
#SBATCH --account=bsc40
#SBATCH --time=24:00:00 # The time you request for the job
#SBATCH --constraint=highmem # To run in highmem nodes

module load singularity

singularity run --cleanenv metaline.sif metaline-generate-config \
    --configFile corachan_kraken2_standard.json \
    --extension fq.gz \
    --basedir /gpfs/projects/bsc40/current/dmajer/metaline-testy-output \
    --reads-directory /gpfs/projects/bsc40/current/okhannous/Clinical_cases/Corachan/raw_data \
    --reference-genome /gpfs/projects/bsc40/current/asukhorukova/index/T2T/T2T \
    --krakendb /gpfs/projects/bsc40/project/pipelines/WGS/KRAKEN2_DB/Broad_gut_microbiome_db \
    --sample-barcode corachan \
    --fastqs PONSJIG_165.E5-NEB-UDI \
    --metaphlan_db /gpfs/projects/bsc40/current/okhannous/Metaphlan4/db \
    --metaphlan_Index mpa_vJun23_CHOCOPhlAnSGB_202307 \
    --n_db /gpfs/projects/bsc40/project/pipelines/WGS/metaPhlan/metaPhla-db/chocophlan \
    --protein_db /gpfs/projects/bsc40/project/pipelines/WGS/metaPhlan/metaPhla-db/uniref

singularity run --cleanenv metaline.sif metaline \
    -r all \
    -j 16 \
    --configfile corachan_kraken2_standard.json