how to make an argument optional in getopts bash

I want to make an argument as optional in getopt bash so that if the user didn't specify it, then it still runs without killing the program. How can i do that. Here is my previous code

while getopts ":l:q:s:e:hg:" opt; do
  case $opt in
    l)
      lincRNAfasta=$OPTARG
    ;;
    q)
      query_species=$OPTARG
      ;;
    s)
      subject_species=$OPTARG
      ;;
    e)
      subject_gff=$OPTARG
      ;;
    h)
      echo "USAGE : open script in text editor"
      exit 1
      ;;
    g)
      subject_genome=$OPTARG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

Sorry, had to update my answer, I misunderstood the question.

I was looking at the documentation for getopts.c which does support ::

But the code that you have works whether I specify 1, 2, or 3 arguments, and in any order.

If it is exiting with an error one reason could be that the variables need to be defined:

#! /bin/bash
lincRNAfasta=
query_species=
subject_species=
subject_gff=
subject_genome=

help='''
  USAGE : open script in text editor
    -l lincRNAfasta
    -q query_species
    -s subject_species
    -e subject_gff
    -g subject_genome
'''

while getopts ":l:q:s:e:hg:" opt; do
  case $opt in
    l)
      lincRNAfasta=$OPTARG
    ;;
    q)
      query_species=$OPTARG
      ;;
    s)
      subject_species=$OPTARG
      ;;
    e)
      subject_gff=$OPTARG
      ;;
    h)
      printf "$help"
      exit 1
      ;;
    g)
      subject_genome=$OPTARG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

echo "doing something else"

if [ -z "$lincRNAfasta" ];then
    echo "its empty"
    echo "lincRNAfasta: $lincRNAfasta"
    echo
else
    echo "not empty"
    echo "lincRNAfasta: $lincRNAfasta"
    echo
fi

if [ -z "$query_species" ];then
    echo "its empty"
    echo "query_species: $query_species"
    echo
else
    echo "not empty"
    echo "query_species: $query_species"
    echo
fi

if [ -z "$subject_species" ];then
    echo "its empty"
    echo "subject_species: $subject_species"
    echo
else
    echo "not empty"
    echo "subject_species: $subject_species"
    echo
fi

if [ -z "$subject_gff" ];then
    echo "its empty"
    echo "subject_gff: $subject_gff"
    echo
else
    echo "not empty"
    echo "subject_gff: $subject_gff"
    echo
fi

if [ -z "$subject_genome" ];then
    echo "its empty"
    echo "subject_genome: $subject_genome"
    echo
else
    echo "not empty"
    echo "subject_genome: $subject_genome"
    echo
fi


# do something once variables have been set
# any variable not set will be empty

echo "doing something else"

Output:

bob@squids:~/Desktop$ ./1.sh -h

  USAGE : open script in text editor
    -l lincRNAfasta
    -q query_species
    -s subject_species
    -e subject_gff
    -g subject_genome
bob@squids:~/Desktop$ ./1.sh -s a -g h -e e -q q
doing something else
its empty
lincRNAfasta: 

not empty
query_species: q

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: h

doing something else
bob@squids:~/Desktop$ ./1.sh -s a -g h -e e
doing something else
its empty
lincRNAfasta: 

its empty
query_species: 

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: h

doing something else
bob@squids:~/Desktop$ ./1.sh -s a -e e -g 123
doing something else
its empty
lincRNAfasta: 

its empty
query_species: 

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: 123

doing something else

Or instead of initializing the variables as empty, you could initialize them as a string like "NOTSPECIFIEDONSTART". And when starting the script you could pass an empty string like -g ''