#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -o bcl2fastq_G172_run2.log
#$ -N bcl2fastq_G172_run2
#$ -pe omp 16
#$ -l mem_per_core=2G
#$ -l h_rt=24:00:00

echo "=========================================================="
echo "Starting on       : $(date)"
echo "Running on node   : $(hostname)"
echo "Current job ID    : $JOB_ID"
echo "Current job name  : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="

#source ~/.bashrc
#module load sratoolkit/2.8.0

#module load basespace-cli/0.8.12.590
#module load bcl2fastq/2.20
#module load cellranger/3.1.0

echo "Copy"

# to download basecall  data
#bs cp //./Runs/191733565/** --exclude "*.jpg" /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/BCL/  &
# 1st run
#cellranger mkfastq --id=G172 --run="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/BCL/" --csv="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172.csv"

# 2nd run without lane
#cellranger mkfastq --id=G172_Run2 --run="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/BCL/" --csv="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172_v1.csv"


echo "Finished  .............. $(date)"