#
# This recipe downloads sequencing data from an SRA run.
#

# Stop on any error. Print the commands as they execute.
set -uex

# SRA folder
SRA_DIR=/export/sra

# NCBI SRA run ID.
RUN=SRR027009

# Library type
LIBRARY=PE

if [ "$LIBRARY" == "PE" ]; then
  # Download the FASTQ data in paired end mode.
  fastq-dump --split-files --outdir $SRA_DIR $RUN

else
  # Download the FASTQ data in single end mode.
  fastq-dump --outdir $SRA_DIR $RUN
fi