Numerical sorting of every column in a file individually using awk

You can do it in a single GNU awk:

gawk -F ',' '
    {
        for(i=1;i<=NF;i++){matrix[i][NR]=$i}
    }
    END{
        for(i=1;i<=NF;i++){asort(matrix[i])}
        for(j=1;j<=NR;j++){
            for(i=1;i<NF;i++){
                printf "%s,",matrix[i][j]
            }
            print matrix[i][j]
        }
    }
' file

• for(i=1;i<=NF;i++){matrix[i][NR]=$i}

Multidimensional array (GNU extension) matrix gets populated, so that matrix[i][j] contains the number of column i, row j.

• for(i=1;i<=NF;i++){asort(matrix[i])}

Sorts each column (GNU extension).

• Finally

  for(j=1;j<=NR;j++){
      for(i=1;i<NF;i++){
          printf "%s,",matrix[i][j]
      }
      print matrix[i][j]
  }
  

Prints a sequence of a[1],, a[2],, ..., a[NF-1],, a[NF]\n for each line.