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Migrate missing nf-core/differentialabundance modules to Seqera containers#11232

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atrigila wants to merge 36 commits intonf-core:masterfrom
atrigila:seqera_containers_diffabundance
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Migrate missing nf-core/differentialabundance modules to Seqera containers#11232
atrigila wants to merge 36 commits intonf-core:masterfrom
atrigila:seqera_containers_diffabundance

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@atrigila
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@atrigila atrigila commented Apr 20, 2026

For: nf-core/differentialabundance#697

  • Migrate modules from biocontainers to Seqera containers
  • Add topic channels if necessary

List of modules:

  • affy/justrma
  • atlasgeneannotationmanipulation/gtf2featureannotation
  • csvtk/join
  • custom/filterdifferentialtable
  • custom/tabulartogseachip
  • geoquery/getgeo
  • proteus/readproteingroups
  • zip

@famosab
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famosab commented Apr 21, 2026

Just out of curiosity: Why did you decide that you want to move away completely from biocontainers? :)

@atrigila
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Hi @famosab, thanks for your question,

deplot.singularityproject tends to make problems from time to time, it would be nice to migrate the remaining modules to use seqera containers.
nf-core/differentialabundance#697

and also: https://nf-co.re/blog/2024/seqera-containers-part-1

@atrigila atrigila marked this pull request as ready for review April 22, 2026 17:28
@atrigila atrigila requested a review from pinin4fjords as a code owner April 22, 2026 17:28
@atrigila atrigila requested a review from grst April 22, 2026 17:29
@atrigila atrigila enabled auto-merge April 23, 2026 15:08
@atrigila atrigila disabled auto-merge April 23, 2026 15:08
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3 participants