https://stackoverflow.com/questions/51412721/how-to-split-an-array-into-chunks-with-jq/51413843#51413629

out.json

[1,2,3]
[4,5,6]
[7,8,9]
[]

partition.jq

#!/opt/local/bin/jq -n -f

def nwise(stream; $n):
  foreach (stream, nan) as $x ([];
    if length == $n then [$x] else . + [$x] end;
    if .[-1] | isnan then .[:-1]                                          ## original
    #if .[-1] | isnan then if (. | length) > 1 then .[:-1] else empty end ## proposed
    elif length == $n then .
    else empty
    end);

nwise(inputs; 3)

run.sh

# note that not all operating systems allow a shebang line to contain more than two words
printf '%s\n' {1..9} | /usr/bin/time -l ./partition.jq -c