#!/bin/tcsh
#SBATCH -N 1
#SBATCH -c 24
#SBATCH --cpus-per-task=24 
#SBATCH --gres=gpu:2
#SBATCH -D ./
#SBATCH --partition=shared
#SBATCH -J Shea
#SBATCH --time=960:00:00
#SBATCH -o Shea.%j.o
#SBATCH -e Shea.%j.e

# Load the module(s)
module load linuxbrew/colsa

# Supernova run for de novo assembly
/mnt/lustre/hale/arthurmelo/Shea/BioInfoSoftwares/supernova-1.2.0/supernova run --id=Shea_S1 \
--fastqs /mnt/lustre/hale/arthurmelo/Shea/RawData10x/S1

# Supernova mkoutput to create FASTA files
/mnt/lustre/hale/arthurmelo/Shea/BioInfoSoftwares/supernova-1.2.0/supernova mkoutput \
--asmdir=/mnt/lustre/hale/arthurmelo/Shea/Assembly/S1/outs/assembly \
--outprefix=S1.Out \
--style=pseudohap \
--minsize=500 \
--headers=full