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DSL2: Provide correct data for upload to sequencing archives (e.g. ENA) #974

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TCLamnidis opened this issue May 2, 2023 · 0 comments
Open

DSL2: Provide correct data for upload to sequencing archives (e.g. ENA) #974

TCLamnidis opened this issue May 2, 2023 · 0 comments
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DSL2 enhancement New feature or request
Milestone
3.0 Augsburg

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@TCLamnidis
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Feature description

Upload of the wrong things to the ENA is a common and deeply frustrating phenomenon in the field. Noone is above it. It would be nice if we had an option in nf-core/eager to run the correct processing of the raw FastQs for upload to the ENA.

As an additional feature, we could also publish the "final" BAMs (used for genotyping) as part of this option, so they can be uploaded as "Analysis Files" if needed.

This should streamline ENA uploads for nf-core/eager users, and help increase reproducibility in the field at large. 🤞
@TCLamnidis TCLamnidis added the enhancement New feature or request label May 2, 2023
@jfy133 jfy133 added this to the 3.0 Augsburg milestone May 26, 2023
@TCLamnidis TCLamnidis changed the title Provide correct data for upload to sequencing archives (e.g. ENA) DSL2: Provide correct data for upload to sequencing archives (e.g. ENA) Aug 23, 2023
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DSL2 enhancement New feature or request
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@jfy133 @TCLamnidis