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# tools
  • n
    Hm, maybe, but I am on an HPC with modules. However, I noticed that at some point the HPC guys seem to have created a singularity module, which seems to actually work
  • s
    yeah, that was my system in the past. But it defined that alias globally
  • s
    (when you loaded the module)
  • n
    Hm, the module I have does not seem to do that
  • n
    does 
    --profile apptainer
    work?
  • n
    If it does it is a secret option
  • n
    --profile         Run tests with a specific profile [docker|singularity|conda]
  • n
    What should I do about this:
    Copy code
    Parsing nf-test error
Parsed nf-test error
╭────────────────────────────────────────────────────────────────────────────────── nf-test error ───────────────────────────────────────────────────────────────────────────────────╮
│ INFO    2026-09-18 10:36:25 DeflaterFactory libdeflate is available; using libdeflate for DEFLATE compression.                                                                     │
│                                                                                                                                                                                    │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error
CRITICAL Ran, but found errors:
          - nf-test failed
          - nf-test failed
    s
    k
    • 3
    • 7
  • d
    Add a linting for docs: github.com/nf-core/tools/pull/4475 Hope I got it right. Related to website PR: github.com/nf-core/website/pull/4409
  • j
    I'd like to be able to migrate my hand-curated ARM-specific container config to the new 
    containers_x
    system, before all the modules have migrated (github.com/nf-core/rnaseq/issues/1920), but right now i think I'm correct in saying that the tooling just wipes and re-creates these files. Proposing a fix: github.com/nf-core/tools/pull/4476
  • s
    The tools have been incredibly slow at several operations, mostly install, update, and patch. I think the root cause is just how many times it checks out its cached clone of nf-core/modules because it (or git) falsely detects it as dirty. What's the best way to troubleshoot this?
    m
    • 2
    • 4
  • e
    When do we plan to bump 
    nft-utils
    in the tempalte? Would be nice to use sanitizeOutput in the local nf-tests
    m
    • 2
    • 2
  • j
    github.com/nf-core/tools/pull/4496 Pre-commit hook to block the 
    .view()
    operator from being committed in the pipeline template. Not sure if this is desirable behaviour for everyone, but I keep accidentally doing it and it would be nice for it to not be happening.
    👌 5
    p
    • 2
    • 1
  • d
    Do not terminate the pipeline after the final retry of OOMs but let running tasks finish: github.com/nf-core/tools/pull/4506
  • l
    Perform params default values interpolation when comparing config to schema. github.com/nf-core/tools/pull/4505
    j
    • 2
    • 2
  • a
    If I have a local module (or I guess a new nf-core one) and I put an 
    environment.yml
    is there a command we have to generate and fetch the container links (singularity + docker) or is this still a manual step?
    m
    m
    • 3
    • 6
  • h
    On a similar note on containers. Was the base image changed on wave? I get new errors which I did not encountered before (kernel in quarto does not start, which could be an updated security config?)
    m
    • 2
    • 5
  • e
    I think we should consider this addition to the template for the error strategy: github.com/nf-core/metatdenovo/pull/588 By @Daniel Lundin! Took me a while to feel it...
    👍 1
    d
    • 2
    • 1
  • o
    Hi! Is there a way to avoid the 
    test_stub_gzip_syntax
    test in 
    nf-core modules lint
    for a specific module? I'm modifying a module to use pigz as a replacement for gzip. The thing is I'm using wave containers, which apparently do not ship 
    gzip
    . So I would like my stub command to be:
    Copy code
    stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    echo "" | pigz > ${prefix}.fastq.gz
    """
    but when linting I get the error:
    Copy code
    test_stub_gzip_syntax: Stub gzip files must use 'echo "" | gzip >' syntax. Invalid patterns found: echo "" | pigz > ${prefix}.fastq.gz
    I'd like to avoid installing 
    gzip
    in the module just because of that... Thanks a lot!
    m
    • 2
    • 4
  • m
    +1 on the above for modules / containers that have 
    bgzip
    rather than 
    gzip
    .
  • m
    My workaround for now is
    Copy code
    touch ${prefix}.fastq
pigz ${prefix}.fastq
    👍 1
  • m
    I saw this and was wondering how the tooling here is working with nf-core? Does this integrate into wave or are they building something else? blog.bioconductor.org/posts/2026-10-07-biofair-cofest
    😮 1
    p
    k
    j
    • 4
    • 28
  • l
    quick look 1
  • r
    https://nfcore.slack.com/archives/CTY8L26C8/p1792058580509369?thread_ts=1792056279.694519&cid=CTY8L26C8 updateing the platform action and allowing v2parser to be enabled. Can I get a review please cat eyes
  • s
    The conda lock files changing name every time we update the module containers makes me sad inside
    💯 2
    m
    • 2
    • 2
  • a
    Is it only me, or do others get 
    nf-core pipelines lint
    constantly changing the formatting of the 
    modules.json
    and the 
    rocrate
    file?
    m
    m
    • 3
    • 5
  • a
    did I get this wrong or is the bot on holiday? github.com/nf-core/tools/pull/4541#…
    m
    • 2
    • 6
  • a
    Is it intended that e.g. 
    nf-core modules bump-versions b
    would bump every single module starting with 
    b
    ? @mashehu you changed this from matching tool or tool/subtool to prefix match, was that intentional?
    m
    • 2
    • 4
  • r
    What is blocking for getting this merged: github.com/nf-core/tools/pull/4518/changes?
    m
    • 2
    • 6
  • j
    Is there a way to have nf-core tools run pipeline linting without trying to check for 
    /pipelines.json
    ?
    m
    j
    • 3
    • 8