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WIP: Added TE annotation workflow#178

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FernandoDuarteF wants to merge 15 commits intonf-core:devfrom
Eco-Flow:repeatmasker
Open

WIP: Added TE annotation workflow#178
FernandoDuarteF wants to merge 15 commits intonf-core:devfrom
Eco-Flow:repeatmasker

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@FernandoDuarteF
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I will update this later.

@FernandoDuarteF FernandoDuarteF added the enhancement New feature or request label Jan 13, 2026
@FernandoDuarteF FernandoDuarteF changed the title Added TE annotation workflow WIP: Added TE annotation workflow Jan 13, 2026
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@FernandoDuarteF
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Added TE annotaion subworkflow back. I deleted it by accident.

@chriswyatt1
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@Alex-cdea, Can you make a PR with your changes?

@Alex-cdea
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@Alex-cdea, Can you make a PR with your changes?

sure, I need to update the README.md

@chriswyatt1
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Plans:
Make into a subworkflow for repeatmasker run. Or use the hite module.
Add flag for local db , instead of downloading.

@chriswyatt1
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Would be good to have some good tests for this too

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4 participants