Add MMseqs Colabfold Search GPU Support#497
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nbtm-sh wants to merge 56 commits intonf-core:devfrom
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…d gpu compiled mmseqs
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Closes #520 |
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keiran-rowell
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Mar 12, 2026
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keiran-rowell
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Looking good.
Can't see/fix your dev merge conflicts since its from your private branch. Once in post release if can resolve conflicts,, tweak language, and it executes consistently, then LGTM
| label 'process_high' | ||
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| container "nf-core/proteinfold_mmseqs_colabfoldsearch:2.0.0" | ||
| container "docker.io/nbtmsh/mmseqs_colabfoldsearch:latest" |
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We should definitely place in quay.io/nf-core (or Seqera wave when it gets to it) when dev is open to merges for v2.1
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Fine for now. Ping Jose a bit before the merge so the container can go to the standard location
| cp ./colabfold_envdb/colabfold_envdb_202108_db_aln.* ./colabfold_envdb_padded/ | ||
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| You should now have a directory structure that looks something similar to this |
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Maybe a quick summary of extensions, something like you must see the db_h files, the .index, etc.
Just to quickly highlight what's not in the pre-DLed DBs.
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Just to quickly highlight what's not in the pre-DLed DBs.
Just a bit confused by this. All the DBs shown here have been downloaded form the mmseqs server. This is just copying the unpadded alignment files to the padded database, as these are also needed
Co-authored-by: Keiran Rowell <42729651+keiran-rowell@users.noreply.github.com>
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@keiran-rowell resolved merge conflicts. Please review my comments |
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Description
This PR aims to add support for GPU accelerated alignment in the colabfoldsearch pipeline.
This is partly awaiting the merge of mmseqs/makepaddedseqdb in nf-core.This will rely on the mmseqs/makepaddedseqdb nf-core module (merged 2025-02-16) to build GPU databases if none are provided.To-Do
Pipeline runs just fine with new GPU accelerated search. The only missing feature is generating the databases if the user does not provide them.
Paths to the container also need to be changed. The upstream dockerfile will need to be rebuilt.