Are some environment variables not respected in DSL2? Are there alternatives?

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Hi everyone, first time poster and just started building some workflows. Would really appreciate some help

It seems that the following environment variables are not respected in DSL2 workflows (tested in Nextflow ≥25.04):

# Expected locations for runtime metadata
export NXF_HOME="${HOME}/.nextflow"
export NXF_LOG="${HOME}/.nextflow/logs/nextflow.log"
export NXF_OUT="${HOME}/.nextflow/output"
export NXF_TEMP="${HOME}/.nextflow/tmp"
export NXF_CACHE="${HOME}/.nextflow/cache"

Despite these being set, Nextflow writes:

  • .nextflow/ (containing cache/, plr/, history, etc.)
  • nextflow.log

to the current working directory, i.e. wherever nextflow run is invoked.

Is this a bug or an intentional design choice (or my own mistake/misunderstanding)?

If it’s by design, doesnt this behavior breaks a fundamental assumption for many environments: that runtime metadata can be centrally redirected and isolated. In our case (proprietary workflows under version control), it means:

  • Source directories may be polluted with internal runtime state
  • Logs and caches appear unpredictably in developer machines - depending on where the workflow was run.
  • Caching and log tracking becomes brittle, as it now implicitly depends on users running the workflow from the exact same path or directory structure

Is there a mechanism to redirect both .nextflow/ and nextflow.log**, similar to how NXF_WORK and NXF_SINGULARITY_CACHEDIR can be configured?

Would appreciate any clarification - or if I’ve just missed something in the docs or something fundamental to how users should be running these workflows when shared (and proprietary to that group).

Thank you very much guys - loving nextflow so far.

2

You can check the proper variable names here: Environment variables — Nextflow documentation

NXF_LOG should be NXF_LOG_FILE
NXF_CACHE should be NXF_CACHE_DIR
NXF_OUT doesn’t seem to exist at all
NXF_TEMP is not related to the files you listed