#reproduciblecomputing — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #reproduciblecomputing, aggregated by home.social.
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake trigger many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake trigger many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake trigger many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake trigger many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake trigger many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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@Dutch_Reproducibility_Network
In fact, I am a #Snakemake co-maintainer and teacher. I was not aware of WorkflowHub - and that was an omission on my part. We actually support and favour this kind of registration: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#uploading-workflows-to-workflowhub
In my original post, I also neglected to mention the integration of WorkflowHub with #RO-Crate and in turn, the integration of RO-Crates with nanopubs. I am actively working on a better support for #nanopub and RO-Crates with @fbartusch. The question, how I teach that stands: The #HPC world (at least my bubble) is not really supportive for #ReproducibleComputing . All #OpenScience shenanigans are frowned upon. And PIs in my vicinity are still on this level: https://phdcomics.com/comics/archive.php?comicid=1531 - so, how do we educate the educators?