01_bcl2fq.sh

#!/bin/bash

# https://slurm.schedmd.com/sbatch.html
# https://wiki.rc.hms.harvard.edu/display/O2

#SBATCH --partition=priority        # Partition (queue) priority
#SBATCH --time=2-00:00              # Runtime in D-HH:MM format, 10:00:00 for hours
#SBATCH --job-name=bcl2fq          # Job name
#SBATCH -c 20			    # cores
#SBATCH --mem=50G           # Memory needed per CPU or --mem-per-cpu
#SBATCH --output=project_%j.out     # File to which STDOUT will be written, including job ID
#SBATCH --error=project_%j.err      # File to which STDERR will be written, including job ID
#SBATCH --mail-type=ALL             # Type of email notification (BEGIN, END, FAIL, ALL)

date

module load bcl2fastq/2.18.0.12

# Harvard Single Cell core script - no trimming of reads
# we use bcl2fastq version 2.18.0.12

# different params - l*
bcl2fastq --use-bases-mask y*,y*,y*,y* \
--mask-short-adapter-reads 0 \
--minimum-trimmed-read-length 0 \
--processing-threads 20 \
--no-lane-splitting \
--sample-sheet $1

# Bauer core 
# bcl2fastq \
# --adapter-stringency 0.9 
# --barcode-mismatches 0 
# --fastq-compression-level 4 
# --ignore-missing-bcls 
# --ignore-missing-filter 
# --ignore-missing-positions 
# --min-log-level INFO 
# --minimum-trimmed-read-length 0 
# --sample-sheet /source/190531_A00794_0025_AHKKFJDMXX/SampleSheet.csv 
# --runfolder-dir /source/190531_A00794_0025_AHKKFJDMXX 
# --output-dir /output/190531_A00794_0025_AHKKFJDMXX 
# --processing-threads 8 --mask-short-adapter-reads 0 --use-bases-mask y*,y*,y*,y*

date