#!/bin/bash
INPUT_DIR=
OUTPUT_DIR=
OUTPUT_FILE=merge.pdf
#INPUT DIR must contain the unzipped ebook file
#unzip file.epub
for i in $( ls $INPUT_DIR ); do
   echo $i
   wkhtmltopdf "$INPUT_DIR/$i" "$OUTPUT_DIR/$i".pdf
done

pdftk `ls "$OUTPUT_DIR"` cat output "$OUTPUT_FILE"

This script enables the conversion of the HTML files available in the ePub format in only one  PDF file

Convert ePub to PDF in Linux command line

Bash

Bash