Fix three dead links in the docs - #538
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- featureCounts moved from bioinf.wehi.edu.au to subread.sourceforge.net. The README link was already updated on dev, docs/output.md still had the old one - MACS callpeak docs are now on macs3-project.github.io, the file no longer exists in the repository - CRAN dropped the web/packages/<name>/README.html layout, cran.r-project.org/package=UpSetR is the stable form All three old URLs return 404 and all three new ones return 200.
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Kevin-Brockers
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Aug 21, 2026
Kevin-Brockers
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Dear @karpovantonme, thanks a lot for your contribution and for fixing the dead links!
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PR checklist
devDescription
Three links in
docs/output.mdreturn 404.bioinf.wehi.edu.au/featureCounts/subread.sourceforge.net/featureCounts.htmlhub.lumenfield.work/macs3-project/MACS/blob/master/docs/callpeak.md#output-filesmacs3-project.github.io/MACS/docs/callpeak.html, the file is gone from the repositorycran.r-project.org/web/packages/UpSetR/README.htmlcran.r-project.org/package=UpSetR, CRAN dropped that layoutThe featureCounts one is already fixed in
README.mdondev, so this bringsdocs/output.mdin line with it.All three old URLs return 404 right now and all three new ones return 200.
How this was found
Pulled every external link out of the markdown files, 304 unique URLs, and requested each one with a browser user agent. Counted only 404, 410 and 451, leaving out 403 and timeouts since those can be my network rather than a dead page.
After this change one 404 remains,
github.com/sofiahaglundin the credits list. I left it alone deliberately: it is a person's account in a thank-you list, and removing someone from credits is not my call.The featureCounts link is dead across the org
The same dead URL appears 22 times in 11 nf-core repositories:
atacseq,callingcards,chipseq,magmap,metatdenovo,modules,nanoseq,nascent,panoramaseq,rnaseq,rnasplice.modulesmatters most, since that one propagates outward. Happy to send the same one-line fix to the others, or tomodulesalone if you would rather handle the propagation your own way. Say which and I will do it.