Hey! I'm a new user of nextflow. Have interest in using taxprofiler and am comparing it to existing bespoke metagenome pipelines in our lab. I'm having a hard time finding out which version of metaphlan the pipeline is using. Does someone have the answer or can point me towards the relevant documentation to uncover the version information?

This is the file you need: https://github.com/nf-core/taxprofiler/blob/master/modules/nf-core/metaphlan/metaphlan/environment.yml The latest release of taxprofiler seems to be using metaphlan v4.1.1

Thanks!

That yuou can also run the test pipeline and you can get the information for two places: `pipeline_info/nf_core_taxprofiler_software_mqc_versions.yaml`: https://nf-co.re/taxprofiler/1.2.4/results/taxprofiler/results-1385e2f895938a5c655011cbbff26a9f3386c82e/pipeline_info/?file=nf_core_taxprofiler_software_mqc_versions.yml Or in the table at the bottom of the MultiQC report in

multiqc/multiqc_report.html

parse all nf-core modules environment yml files! 😛

What if you have multiple tools in there

true, could do only for matching name-command ones, but I get your point!

Perhaps publishing tool versions to the website on release would be useful?

I guess could just take the contents of

nf_core_taxprofiler_software_mqc_versions.yml

from the megatest run would be sufficient... but the megatests are not that reliable annoyingly

From a user perspective the versions of tools used in the pipeline is quite important when assessing which pipeline/methods to use. I think it would be very beneficial to have, at least the major, version numbers readily displayed in the documentation somewhere.