Hello everyone! I have a small question. So, if I am running the mag pipeline, can I get information about what exact parameters are used for each tool? In the modules section, I tried to look, but for most of the tools, I was not able to get the exact parameters.

Hello! If you're already running mag and want to know the command executed for a specific tool, you can take a look at the execution directory of the process (inside

work/

). There you should find a

.command.sh

file containing the exact command executed. If you want to get that info before running mag, you can take a look at github.com/nf-core/mag/blob/…/modules.config. There you should look for

ext.args

, this parameter adds cli options to the process itself. Some of this args come directly from pipeline parameters, as you can see.

Thanks! I looked into those. I was wondering if there is any documentation or built-in report that collects the exact parameters used for all tools in one place. Similar to the software versions report, is there an equivalent summary for tool parameters, or is inspecting the individual .command.sh files the only way? Again thank you for reply!

.command.sh files are the best bet because they are the files that are actually executed. That file is a combination of the module code (that usually only contains generic parameter such as how many threads that process takes etc) and the critical params are usually set via modules.config as Diego said before. Afaik there is no summary documentation or report for all exact commands. Pipeline params are collected in results/pipeline_info/*.json though.

Okay, thank you both for your help!