btw I have another plugin waiting for approval 🙂 nf-lims

both naming and description looks a bit too generic. what lims are supported? is it compliant with some specific api ?

It supports a generic REST API... maybe should I change the name? I added more documentation to https://github.com/biocorecrg/nf-lims

Agree it still sounds a bit unclear. Setting the base URL is one thing, but what are the different API endpoints? What kind of auth? LIMS are a hugely heterogenous group of software. I think it might be better to at least point to a reference LIMS that it is compatible with, if possible?

You are right. I will try to make it better. The idea is to send a payload to a rest API with a token (it is working for us but of course is not so general). I'll keep it private for now and let's see if I can make it for general interest. Thanks anyway!

Thanks! 🙏🏻

Let me talk to the developer of our LIMS to see if we can make it better. The idea is that the pipeline ends and sends a status + info. We are "connecting" several pipelines so it good to have a plugin instead of a function :)

@Luca Cozzuto: Nextflow already has a weblog plugin that sends logs to a given URL. You could use that existing plugin and add something in the middle that filters the “pipeline completed” events and forwards to your backend with a modified payload as needed. You may be able to implementing the filtering + transformation in logstash

Yep I saw that but was thinking that adding a payload was difficult and also was done more for sending the logs of the pipeline. I just need that is triggered at the very end with just status and payload

I've actually been thinking along the same lines, partly inspired by nf-slack. The challenge is you basically need to write a generic POST request mechanism, which can have arbitrary content. For example, in your code you have success or failure, which is great but in a previous LIMS I had a whole range of statuses that stated where the sample was in the flow, e.g. pending, sequenced, aligned, variant-called, interpreted, submitted. It's really tough to support all of these use cases; you basically need to write your own DSL in the config 😆 So like Phil, I think this should be called something specific for you. Call it nf-crg-lims or something and keep it specific for your use case. Do one thing well!

So now my question will be... Can I have it somewhere so that I can download it like the nextflow registry? Like a private registry on GitHub or whatever?

You can have it on the registry I think, just call it

nf-crg-lims

instead of

nf-lims

here a new submission so: nf-crg-genomics-lims Thanks!