Snakemake – A framework for reproducible data analysis

Re:Snakemake – A framework for reproducible data analysis by tetris11 on Saturday July 15, 2023 @08:24AM (#36735948)

Its fantastic but it doesn't scale laterelly particularly well, compared to just Make.

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Re:Snakemake – A framework for reproducible data analysis by ta988 on Saturday July 15, 2023 @11:33AM (#36737723)

What dimension are you referring to?

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Re:Snakemake – A framework for reproducible data analysis by tetris11 on Saturday July 15, 2023 @12:07PM (#36738122)

Large scale reproducibility was a problem a few years back for one. Conda and containers were a constant problem for us back then, especially if you had multiple NGS tools running in different environments. This has probably been solved by now, but we went with another workflow system

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Re:Snakemake – A framework for reproducible data analysis by bafe on Saturday July 15, 2023 @03:19PM (#36740047)

Nextflow seems to scale very well

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Re:Snakemake – A framework for reproducible data analysis by tetris11 on Sunday July 16, 2023 @05:48AM (#36745173)

We went with Nextflow and Galaxy

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Re:Snakemake – A framework for reproducible data analysis by bafe on Monday July 17, 2023 @03:52PM (#36763141)

You can't go wrong with nextflow. I heard a lot of scientists complaining that it's too hard to understand, but honestly the DSl and the scheduling model (flow based) is just great

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Re:Snakemake – A framework for reproducible data analysis by ta988 on Saturday July 15, 2023 @11:56PM (#36743462)

Agreed, Conda has always been a nightmare to maintain and redeploy, whatever you put it in.

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