What is the recommendation for including Fragpipe in standartized workflows (snakemake/nextflow)?

[CrystalColeCrystal]

Hello!

I'm interested in you recommendation on how Fragpipe/MSfragger should be included in standartised workflows run with snakemake or nextflow? Should it be included as fragpipe or as msfragger? I'm intereseted in my workflow being HPC-friendly, so UI is really not needed. Is Fragpipe -headless mode equivalent to command-line MSfragger or no? Also, since MSfragger license does not permit distributing its Docker/Singularity images as discussed here #1888 what is the easiest way to ensure reproducibility of said workflow?

Thank you so much for your help!

[fcyu]

We have a FragPipe Docker image here https://hub.docker.com/r/fcyucn/fragpipe

You can run FragPipe in command line using the "headless" mode.

FragPipe and MSFragger are two different things.

Regarding MSFragger, you can not distribute any docker/singularity/snakemake/nextflow or other types of images due to the license.

Since MSFragger is just a single jar file, I don't see any issue regarding the reproducibility.

Best,

Fengchao