how to make an argument optional in getopt bash - bash

Question

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

Answer 1

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 ''