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Hi MultiQC experts, switching from 1.21 to 1.25 so...
# multiqc
s
Hi MultiQC experts, switching from 1.21 to 1.25 some major custom content disappeared, for the issue see https://github.com/nf-core/pangenome/issues/224. For visual clarity, I appended 2 screenshots. Any help appreciated 🙂
😱 1
✅ 1
My wild guess: All custom content file names start with 
DRB1-3123.fa.gz
and with the new version MultiQC is treating these all like the same sample and not as custom content names.
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/// MultiQC 🔍 v1.25.1

            config | Loading config settings from: multiqc_config.yml
     version_check | MultiQC Version v1.26 now available!
       file_search | Search path: /home/heumos/git/pangenome/work/0c/5bc476fe46465ab6a0e1dd78b6719d

              odgi | Found 1 report
    custom_content | HTML plot type found with more than one dataset in nf-core-pangenome-methods-description
    custom_content | nf-core-pangenome-methods-description: Found 1 sample (html)
    custom_content | HTML plot type found with more than one dataset in nf-core-pangenome-summary
    custom_content | nf-core-pangenome-summary: Found 1 sample (html)
    custom_content | Image plot type found with more than one dataset in DRB1-3123
    custom_content | DRB1-3123: Found 1 sample (image)
     write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag

     write_results | Data        : multiqc_data
     write_results | Report      : multiqc_report.html
     write_results | Plots       : multiqc_plots
           multiqc | MultiQC complete
The MultiQC log.
p
'cc @Vlad Savelyev when you get a moment
@Simon Heumos we're building up to quite a large release this week, so may take a few days to get to this 🙏🏻
s
got it, thanks @Michael Heuer how about we roll back MultiQC to 1.21 on 
dev
until we know more?
v
Will take a look now
🎉 1
Any chance you would be able to share the inputs to multiqc for me to reproduce the issue easier?
p
(ie. the work directory)
s
sure, give me a sec
5bc476fe46465ab6a0e1dd78b6719d.zip
5bc476fe46465ab6a0e1dd78b6719d.zip
u need anything else @Vlad Savelyev?
v
Unfortunately the nextflow work directory contains just symlinks, not the actual files
s
lol
I forgot
odgi_viz.zip
odgi_viz.zip
DRB1-3123.fa.gz.gfaffix.draw_multiqc.png
these should be all relevant PNGs
DRB1-3123.fa.gz.gfaffix.og.stats.yaml,DRB1-3123.fa.gz.seqwish.og.stats.yaml
DRB1-3123.fa.gz.seqwish.og.stats.yamlDRB1-3123.fa.gz.gfaffix.og.stats.yaml
sorry @Vlad Savelyev
v
Thank you 🙏
s
methods_description_mqc.yaml
methods_description_mqc.yaml
workflow_summary_mqc.yaml
workflow_summary_mqc.yaml
nf_core_pangenome_software_mqc_versions.yml
nf_core_pangenome_software_mqc_versions.yml
this should really have been everything
v
Seem to be woking for me
s
thanks for taking a look
v
Note that this is 1.26
s
hmm
v
Let me take a look at 1.25
s
1.25.1
v
Yep 1.25* was broken
I now remember fixing this for 1.26
In any case, if you pin to 1.26, it should work. But let me know if something is still does not look good!
s
alright, now I know a way forward will ping you here about the outcome thanks @Vlad Savelyev!
☺️ 1
p
Note that #CJRH30T6V has already been updated, so just running 
nf-core modules update multiqc
should fix it in that case
🎉 1
s
1.26 fixes the issue, thanks again!
p
Great! 🎉
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