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# nf-core-utils
  • m
  • m
    and another one for #C073ZDLNC92 https://github.com/nf-core/nf-core-utils/pull/28
  • m
    @Edmund I have 4 PRs that @Nicolas Vannieuwkerke approved, can you have a look and see if you have comments, I'd love to be able to merge in and release as it's a blocker for me now
    salute 1
    e
    n
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  • m
  • m
    That would help making better validations for the other PRs I have in the oven
  • m
    Thanks @Edmund for the reviews. Do you think we can get a release, I'm happy to talk about the things for #C073ZDLNC92 at another point, I know you disagree with my views on that, and I am not hell-bent on it, but I have some nice arguments as to why I want to do it that way.
    ❤️ 1
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  • m
    I'm trying my best at https://github.com/nf-core/nf-core-utils/pull/31 I will be totally honest, and say that I have no idea what I'm doing, but I'll figure it out on the way.
    n
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  • l
    Why hurt me like this ? 🥲 > Failed requirement - Plugin nf-core-utils@0.4.0 requires Nextflow version >=25.10.0 (current 25.04.0)
    m
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  • j
    HOW DID I NOT KNOW ABOUT THIS CHANNEL
    🤣 1
  • j
    Random idea: would this plugin be a place to make custom error classes for nf-core specific things? I'm thinking of instead of just using the nextflow default 
    error
    and 
    log.warn
    , we could have a special function that appends the name of the pipeline or module to the beginning
  • j
    I'm thinking something like 
    [nf-core/sarek] ERROR: you made a mistake
    or 
    [SAMTOOLS_VIEW] WARN: you missed something, check output carefully
  • j
    I ask as it might make it easier to help users recognise where the error is happening, e.g. is it a nextflow error? A pipeline validation check error?
  • j
    A special function oculd try and do the special formatting, and auto-inject the pipeline/subworkflow/module name? to be clear I can't code this (neither skill not time currently), but I wonder if it would be useful
  • j
    OR would be this be better for the template?
  • m
    that's a nice idea
  • j
    How feasible is it do you think?
  • j
    Can you somehow how pull the filename 'context' from within the script file itself, for example?
  • j
    (if you know)
  • n
    interesting idea! Getting the pipeline name is a no brainer but the module names might be more difficult (unless we give the function an option for that)
    👍 1
  • j
    I'll make an issue 🙂
    🙏 2
  • j
  • n
    I fixed a function to be compatible with the new parameter types in nextflow: https://github.com/nf-core/nf-core-utils/pull/39
  • n
    I also noticed some heavy usage of the standard Java 
    File
    and 
    Path
    in the plugin. This makes the plugin incompatible with cloud file paths for example. It's better to use the built-in 
    Nextflow.file()
    function with all Nextflow file operation methods.
    ✅ 1
    m
    • 2
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  • a
    Hi everyone! Could we have a patch release of nft-utils soon? I am trying to fix an issue in demultiplex that requires changes in an nf-core module, but I cannot make the updates to the snapshots due to an error with 
    sanitizeOutput()
    in the nft-utils v1.1.1 used in nf-core modules. There is already a fix in place in nft-utils github.com/nf-core/nft-utils/pull/85 which I think would solve this issue.
    m
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  • m
    @Matthias De Smet is this PR still active, needed or being worked on? https://github.com/nf-core/nft-utils/pull/65
    m
    n
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  • m
    @Louis Le Nézet I have made minor comments on https://github.com/nf-core/nft-utils/pull/86
  • m
    @Matthias De Smet from what I from https://github.com/nf-core/nft-utils/issues/87 There is still an issue on top of the one fixed by https://github.com/nf-core/nft-utils/pull/85
    m
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  • e
  • m
    Adding functionnalities for #C073ZDLNC92 https://github.com/nf-core/nf-core-utils/pull/83/changes
  • m
    And hopefully release