#!/bin/sh
#SBATCH --mail-user=adalena.nanni@ufl.edu
#SBATCH --job-name=compare_species
#SBATCH --account=mcintyre
#SBATCH --qos=mcintyre-b
#SBATCH --mail-type=FAIL
#SBATCH --output=/blue/mcintyre/share/transcript_distance/scripts/dros_ref/SLURM_LOGS/nf_compare_%A.out
#SBATCH --time=48:00:00
#SBATCH --ntasks=1              # single cpu core
#SBATCH --cpus-per-task=1
#SBATCH --mem=1gb              # per processor memory

## run nextflow comparing species

## directory where nextflow scripts are
NF=/blue/mcintyre/share/transcript_distance/scripts/dros_ref
REPORT=/blue/mcintyre/share/transcript_distance/scripts/dros_ref/nextflow_reports
    mkdir -p ${REPORT}

## create java temp dir
mkdir -p /blue/mcintyre/share/transcript_distance/dros_analysis/ROZ_NF

module load nextflow/20.07.1

export _JAVA_OPTIONS="-Djava.io.tmpdir=/blue/mcintyre/share/transcript_distance/dros_analysis/ROZ_NF"

nextflow run ${NF}/NF_compare_species_ref_02avn.nf \
    -c ${NF}/nextflow_compare_mel_sim_ref.config \
    -resume