Hi,
Without checking if this has been asked before, I was wondering if there is a quick way to include Nextflow workflow status information (e.g., duration, failedCount, succeedCount, etc.) in the MultiQC report as the final section.
Would it be possible to achieve this using custom content?
Thanks
Hi @jinfinance,
Generally speaking, MultiQC runs within the Nextflow workflow, at which point that information is not available - so no.
That said, if you’re running MultiQC manually after the workflow completes, then sure - should be possible.
Phil
good point !
OK, what about just capturing the command line parameters used in the nextflow run, and display them at the bottom of the MultiQC report. Any general suggestions ?
Thanks !
We had some discussion around that in nf-core (see PRs here and here), but the end I think that the consensus was that all this information was already captured in the Nextflow report, so no need for us to duplicate it.
But there may well be some useful code there if you’re interested.
Note that this is all resolved parameters, not the CLI params which is what you asked for. Nextflow has a bunch of constant variables which may do what you want, including workflows.commandLine
As they’re in the Nextflow run time, you should be able to dump these into a YAML file and then feed that to a MultiQC process to get it into the report, via Custom Content.
Phil
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