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Samtools for ARM64 #129

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brainstorm
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In line with our discussions with @scwatts, this PR bumps samtools to bioconda's 1.21 to address build failure (https://wave.seqera.io/view/builds/bd-ea05fc7cfdaac5fc_3) due to missing linux-aarch64 package.

This is for testing purposes only, whether to release under 1.0.1 and/or 2.0.0 remains under @scwatts discretion ;)

/cc @mmalenic @ohofmann

…e galaxy and biocontainers with older versions for now
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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: 3.0.2.
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.

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scwatts commented Feb 6, 2025

Apologies @brainstorm, I mistook those messages as being related to potential changes for a hypothetical minor release I was considering specifically for ARM64 support rather than actively testing out potential solutions on the dev branch. I don't think dev is the best place to trial / test these types of changes - sorry for the misunderstanding.

I'd like to coordinate with you more closely on this to first build a complete understanding of which tools used by oncoanalyser lack ARM64 support (including combinations, see here), agree on how to address these support gaps (e.g. add/update Conda recipes or indeed update software versions), and create an inventory of required changes. Once that is done those changes can be made locally and ARM64 support confirmed through several test runs.

Let's discuss this more directly together so we can progress this piece of work!

@scwatts scwatts closed this Feb 6, 2025
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