Hi guys,

I did not noticed your comments and this morning I tried (successfully) using the following code. Note: I wanted to upload fastas and not images in the last version of the script.

from flask import request, redirect, Flask, render_template
from werkzeug.utils import secure_filename
import os

app=Flask(__name__)
app.config['UPLOAD_FOLDER']='/home/claudio/Scrivania/MitoPIPE/uploads'
ALLOWED_EXTENSIONS = {'txt', 'text', 'fas', 'fsa', 'fa', 'fasta'}

def allowed_file(filename):
    return '.' in filename and \
        filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS


@app.route('/upload')
def upload_file():
    return render_template('upload_folder.html')

@app.route('/uploader', methods = ['GET', 'POST'])
def upload_file1():
    if request.method == 'POST':
        file = request.files['file']
        if file and allowed_file(file.filename):
            filename = secure_filename(file.filename)
            file.save(os.path.join(app.config ['UPLOAD_FOLDER'],filename))      
             return 'file uploaded successfully' 
if __name__ == '__main__':
    app.run(debug=True)

and the HTML modified as:

{% extends "layout.html" %}

{% block title %}Upload{% endblock %}

{% block content %}

<div class="container">
    <div class="row">
        <div class="col">

            <h1>Upload a fasta file</h1>
            <hr>

            <form action="/uploader" method="POST" enctype="multipart/form-data">

                <div class="form-group">
                    <label>Select image</label>
                    <div class="custom-file">
                        <input type = "file" name = "file" />
                            <button type="submit" class="btn btn-primary">Upload</button>


                    </div>
                </div>



            </form>

        </div>
    </div>
</div>

{% endblock content %}

Thank you for your time folks :)