Hi Steffen and everybody, I also use Nextflow at work, and indeed, it makes it very easy to run a pipeline many times. Also, Nextflow is a single Java executable, which makes it easy to deploy anywhere Java is already installed.
You probably also saw the nf-core repository of modules and pipelines. I like the way they are organised and find them empowering. The community is very nice too. BUT With my Debian background it is very hard for me to adapt to the conda / biocona / quay / galaxy ecosystem. I just can not figure out who is responsible for what, no idea how long the whole thing will be supported, where is the source code used to build the the packages into Docker images in to Singularity images, etc. Not to mention that the whole paradigm behind "one tool, one minimal image" deprives me from all the Unix tools that I use to enjoy on in a Debian context. In bioconda you have no idea whether sed is from GNU of from busybox unless you try it or dig for a package recipe in GitHub... NOT TO MENTION THAT Everybody expects that these images will stay forever and for free at the URL where they are, while I have not seen any evidence of an organisation promising that it will really happen for at least a decade... Without these images and the receipes to create them (remember the singularity <- docker <- conda <- GitHub fragmentation), the hope that these pipelines provide reproducibility in the long term is wishful thiking. SO Against the stream of minimising image size to the bone while processing terabytes of sequencing data, I thing that Debian Med images with all of our packages installed would be a useful alternative in many cases. I am already doing something along the lines on our HPC cluster to turn our packages into environment modules (lmod). https://github.com/oist/BioinfoUgrp/blob/master/DebianMedModules.md#creation-of-a-new-singularity-image The size of the images is a bit less than 8 GiB, and I make a new image at each point release. Would there be some interest to make such images in a more official way ? Have a nice day, Charles -- Charles Plessy Nagahama, Yomitan, Okinawa, Japan Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from home https://framapiaf.org/@charles_plessy - You do not have my permission to use this email to train an AI -
