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Bismark methylationextractor supplies unused "counts" argument #3644

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robsyme opened this issue Jul 14, 2023 · 1 comment
Open

Bismark methylationextractor supplies unused "counts" argument #3644

robsyme opened this issue Jul 14, 2023 · 1 comment

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@robsyme
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robsyme commented Jul 14, 2023

In our module, we call the bismark_methylation_extractor executable with a --counts argument, but I don't see any reference to this argument in the bismark_methylation_extractor documentation or in the --help commands.

https://github.com/nf-core/methylseq/blob/81f989c93e866a9b0bd0d9584e077b9b8f78affe/modules/nf-core/bismark/methylationextractor/main.nf#L38-L45

This may be fair game for removal.
@robsyme
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robsyme commented Jul 14, 2023

Thanks to Anand Venkatraman for reporting!

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