Stacks: process_radtags on SLURM

jobarray_process_radtags.sh

#!/bin/bash
#SBATCH --time=06:00:00
#SBATCH --mem=16G
#SBATCH --mail-user=andersgs@gmail.com
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=REQUEUE
#SBATCH --mail-type=ALL

module load singularity/2.4

MAPPING_FILE=$1
LINE=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $MAPPING_FILE)

echo $LINE | while read SAMPLE READS BARCODES PAIRED ENZYME
do
  OUTDIR=/path/to/samples/${SAMPLE}
  mkdir -p ${OUTDIR}
  if [ "${PAIRED}" = "TRUE" ];
    then
      PAIRED="--paired"
    else
      PAIRED=""
  fi

bash process_reads.sh --reads ${READS} --barcodes ${BARCODES} --enzyme ${ENZYME} --output ${OUTDIR} ${PAIRED}

process_radtags.sh

module load singularity/2.4

IMAGES=<path/to/singularity/images>
STACKS=stacks.img
PAIRED=''

USAGE="USAGE:\n\trun_process_radtags.sh --reads path/to/reads [--paired] --output path/to/output --barcodes path/to/barcodes --enzyme enzyme"

while [[ $# -gt 0 ]]
do
  key="$1"
  case $key in
    -r|--reads)
    READS="$2"
    echo "Found READS."
    shift
    shift
    ;;
    -o|--output)
    OUTPUT="$2"
    echo "Found OUTPUT."
    shift
    shift
    ;;
    -b|--barcodes)
    BARCODES="$2"
    echo "Found BARCODES."
    shift
    shift
    ;;
    -e|--enzyme)
    ENZYME="$2"
    echo "Found ENZYME."
    shift
    shift
    ;;
    -p|--paired)
    PAIRED='--paired'
    echo "Found PAIRED."
    shift
    ;;
  esac
done

ERROR=0

if [[ -z "${READS}" ]]
then
  echo "Please supply path to reads (-r | --reads)."
  ERROR=1
fi

if [[ -z "${OUTPUT}" ]]
then
  echo "Please supply path to output (-o | --output)."
  ERROR=1
fi

if [[ -z "${BARCODES}" ]]
then
  echo "Please supply path to barcodes file (-b | --barcodes)."
  ERROR=1
fi

if [[ -z "${ENZYME}" ]]
then
  echo "Please supply the enzyme used (-e | --enzyme)."
  ERROR=1
fi

if [[ "${ERROR}" -ne "0" ]]
then
  echo -e ${USAGE}
  exit 1
fi

echo "Successfully parsed variables."
echo "Starting run..."

START=$(date +%s.%N)
singularity run --bind /project/6005977 --bind /scratch/andersgs ${IMAGES}/${STACKS} process_radtags -p ${READS} ${PAIRED} -o ${OUTPUT} -b ${BARCODES} -e ${ENZYME} -r -c -q
END=$(date +%s.%N)
DIFF=$(echo "($END - $START)/60" | bc)
echo "Program took ${DIFF} minutes to complete."

INSTRUCTIONS

Before you start, you need to prepare a TSV file where each line is a different library, and has five fields in the following order:
SAMPLE: A unique sample name (with no spaces or /)
READS: the full path to the FASTQ files
BARCODES: the full path to the Barcode file
PAIRED: TRUE or FALSE if the library is paired-end
ENZYME: The name of the enzyme used (e.g., SbfI)

A line in the file might look like this:

Lib1\t/home/user/reads/lib1\t/home/user/barcodes/lib1.txt\tTRUE\tSbfI

1. Create a folder to store the Singularity images
2. Download the Stacks singularity image: singularity pull --name "stacks.img" phgenomics-singularity/stacks
3. Edit process_radtags.sh to make sure the path to the Singularity images is correct
4. Edit the last line of jobarray_process_radtags.sh to make sure the path to process_radtags.sh is correct AND line 18 to make sure it points to an existing folder to store the output.
5. Submit the job to SLURM queue with the following:
   sbatch --array 1-<number of libraries> jobarray_process_radtags.sh </path/to/mapping_file>