We would like to distribute multiqc_report.html as...
# multiqcm
Michael Heuer
02/04/2026, 3:49 PMWe would like to distribute multiqc_report.html as-is but the Report generated on and Workflow Summary sections leak too much about our infrastructure: fusion mount points, bucket names, path prefixes, etc. Though clobbering these sections in the generated HTML works for now, I wonder if it might be possible to mask things ahead of time? Something like
--mask-path-prefix--use-relative-paths-onlyp
Phil Ewels
02/04/2026, 4:03 PMYou mean the bit at the top of the report saying what the input paths were for running MultiQC? There a MultiQC config option to just not include that bit. It's kind of meaningless for Nextflow pipelines anyway..
Phil Ewels
02/04/2026, 4:03 PMOr are these paths etc. elsewhere in the report?
Phil Ewels
02/04/2026, 4:03 PMPhil Ewels
02/04/2026, 4:03 PM Copy code
show_analysis_paths: FalsePhil Ewels
02/04/2026, 4:04 PMAh sorry, you said: "Workflow Summary sections" - this is an nf-core thing and not controlled within MultiQC at all..
Phil Ewels
02/04/2026, 4:05 PMI guess it's the params that are the issue? Coming from here: https://github.com/nf-core/tools/blob/fee44dae3fb1f86561f8ee11a62eb6207804dc5d/nf_[…]ine-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
Phil Ewels
02/04/2026, 4:06 PMThe params themselves come from nf-schema: https://nextflow-io.github.io/nf-schema/latest/parameters/summary_log/#paramssummarymap
Phil Ewels
02/04/2026, 4:07 PMThat'd probably be your easiest route here: update the nf-schema plugin to sanitise the params map with any paths. Then you can configure any Nextflow / nf-core pipeline to use that newer version of the plugin without needing to edit any pipeline code.
Phil Ewels
02/04/2026, 4:07 PMAll via Nextflow config only
m
Michael Heuer
02/04/2026, 4:25 PMThanks, Phil!
The Report generated on section is this bit at the top
Michael Heuer
02/04/2026, 4:26 PMThe nf-schema approach sounds reasonable, I'll look into that
Michael Heuer
02/04/2026, 5:43 PMp
Phil Ewels
02/04/2026, 9:23 PMyeah, set the config I linked and the "based on data in.." bit should dissapear
Phil Ewels
02/04/2026, 9:24 PMNice work on the PR! Over to #C056RQB10LU for the rest of that if needed 🙂
m
Michael Heuer
02/23/2026, 6:48 PMSorry, I'm not sure how to provide these config parameters to multiqc from within a nf-core workflow
Copy code
show_analysis_paths: False
show_analysis_time: False--cl-config Copy code
withName: 'MULTIQC' {
ext.args = { [
params.multiqc_title ? "--title \"$params.multiqc_title\"" : '',
'--cl-config "show_analysis_paths: False, show_analysis_time: False"'
].join(' ').trim() }
}p
Phil Ewels
02/24/2026, 3:25 PMI think that the template has a MultiQC config file built in already? You can just append to that.
gratitude thank you 1
Phil Ewels
02/24/2026, 3:26 PMIf editing a pipeline
m
Michael Heuer
02/24/2026, 3:44 PMI need something at runtime, I don't want to have to maintain fork all the pipelines we use
Michael Heuer
02/24/2026, 3:44 PMAh, this works! inline YAML formatting issue above
Copy code
ext.args = { [
params.multiqc_title ? "--title \"$params.multiqc_title\"" : '',
'--cl-config "show_analysis_paths: False\nshow_analysis_time: False"'
].join(' ').trim() }p
Phil Ewels
02/24/2026, 4:45 PMI think that there should be a
--multiqc_config2 Views