Fastq-dump script download X spots or all

Question

Im trying to write a script where an optional input of -X flag can be used, or if that info is not available download all reads.

my script as follow:

# usage : bash dump_qc.sh <run id> <number of reads>

#run id variable.
SRR=$1

#maximum reads variable
X=$2

fastq-dump --split-3 -X ${X} ${SRR}

So, if I run the script

bash dump_qc.sh SRR1234 100

Will download 100 reads from the specified SRR file.

What I would like to do is to make the second argument optional, if not specified download the whole data set!

Answer 1

You don't need to copy your arguments into variables, you can just use $1 directly. Anyway, this should be enough:

#!/bin/bash
# usage : bash dump_qc.sh <run id> <number of reads>

if [ -z $1 ]; then
  echo "ERROR: at least one argument need to be given!" >&2
  exit 1
fi

if [ ! -z $2 ]; then
    x="-X '$2'"
fi

fastq-dump --split-3 "$x" "$1"