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new list of proteomics modules #5599

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rolivella opened this issue May 14, 2024 · 9 comments
Open

new list of proteomics modules #5599

rolivella opened this issue May 14, 2024 · 9 comments
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@rolivella rolivella added the new module Adding a new module label May 14, 2024
@mirpedrol
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This issue tracks the proteomics modules that should be added to nf-core.

Some of them are available as local modules from the quantms pipeline, which have to be converted to nf-core modules.
For the rest of the modules we link the tool, if the container is available and test data.

Contributors are welcome 🙂

@jonasscheid
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jonasscheid commented Sep 11, 2024

Nice! I already started with a couple of openms tools that we use: nf-core/mhcquant#296

@jonasscheid
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@rolivella bruker recommends to use tdf2mzml for parsing .d -> mzML. Might be worth to focus on that tool, there is also an existing docker container on dockerhub

@jonasscheid
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btw peptideindexer already exists: #4642

@rolivella
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rolivella commented Sep 12, 2024

@jonasscheid ok! we can start with this bruker conversor. Where is the container?

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@jonasscheid
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@rolivella Do you have experience with timsconvert? :) Out of curiosity

@rolivella
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No, I'm afraid I don't have any experience...

@rolivella
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rolivella commented Oct 7, 2024

@jonasscheid maybe you could be interested in this discussion: gtluu/timsconvert#64

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