@app.route('/assemblies', methods=['GET', 'POST'])
def assemblies():
    if request.method == 'POST':
        if request.form['submit'] == 'runFile':
            #os.startfile("/static/run.bat")
            text = "... running ..."
            filepath="/static/run.bat"
            p = subprocess.Popen(filepath, shell=True, stdout = subprocess.PIPE)
            stdout, stderr = p.communicate()
            return render_template('assemblies.html', text=text)
        else request.form['submit'] == 'process':
            [do other stuff]
    elif request.method == 'GET':
        return render_template('assemblies.html')

<div class="container">
    <form action="/assemblies" method="post"> ASSEMBLY <br>
        <select name="Layer">
            <option value="1">1</option>
            <option value="2">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
            <option value="5">5</option>
        </select><br>
        <button type="submit" name="submit" value="process"> Process </button>
        <button  type="submit" name="submit" value="runFile"> Run </button>
    </form>
</div>

start /d "static" myFile.exe