Retrieve information from .command.log and add as table


I am using a tool not yet available as MultiQC module as far as I see (picard liftover). As far as I can tell, the tool does not write it’s own log file, but prints everything interesting directly. Nextflow captures this in the .command.log file (edit: managed to at least dump this into its own file to publish alongside the results). Is there a way I can fetch this info with MultiQC and display it as a table. Does anyone have an example flying around on how to do it?

I think that the safest way to do this is to capture the STDOUT to a dedicated file, rather than relying on .command.out. You can do this by redirecting it, eg.

picard [options] > mysample_picard_liftover.log

Once you have the file, it’s likely not super trivial to convert it into a table for a MultiQC report. Picard outputs are typically not in a standard format that you can pipe directly into Custom Content (eg. not a TSV file etc). So I think that your best bet is really to write proper MultiQC support for it (or creating an issue for it with some example outputs). The source code for the various Picard tool support in MultiQC is here: