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this is a really underdocumented feature that this extension supports, wanted to share it with people. i've never written and shared a blog post like this before so feel free to give me tips about documenting steps or point out any errors i made. i kinda take docker knowldge for granted, not sure if i should avoid that. here's the contents:

I came across documentation for this in the readme for the FreshRSS extension YoutubeChannel2RssFeed. The method involves running an instance of the Youtube-operational-API (there was a public instance that has been cease and desisted by Google, see here) and plugging the extension into it.

YoutubeChannel2RssFeed Extension

TL;DR install this extension

git clone https://github.com/cn-tools/cntools_FreshRssExtensions.git
cd cntools_FreshRssExtension
cp -r xExtension-YouTubeChannel2RssFeed <your_freshrss_data_directory>/config/www/freshrss/extensions

Youtube-operational-API instance

Here's a Docker compose.yml for running both

services:
  freshrss:
    image: lscr.io/linuxserver/freshrss:latest
    container_name: freshrss
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=America/Los_Angeles
    volumes:
      - ./freshrss/config:/config
    ports:
      - "8811:80""
    restart: unless-stopped
  youtube-operational-api:
    container_name: freshrss-yt-o-api
    image: benjaminloison/youtube-operational-api:latest
    restart: unless-stopped
    ports:
      - "8812:80"
    depends_on:
     - freshrss

Configuring extension

In FreshRSS, log in as admin and go to Configuration > Extensions. Turn on YoutubeChannel2RssFeed under User extensions and click the gear to configure.

Set Youtube Shorts to be marked as read or blocked completely. Enter the URL for your yt-o-api instance. Based on the above compose file it would be http://freshrss-yt-o-api:8812. Submit changes.

For me this worked immediately, no shorts ever show up in FreshRSS for my Youtube feeds. I haven't seen this documented anywhere else so I wanted to mirror it somewhere.