Skip to content

Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from config#804

Merged
ramprasadn merged 1 commit into
release300from
removenxf
Apr 8, 2026
Merged

Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from config#804
ramprasadn merged 1 commit into
release300from
removenxf

Conversation

@ramprasadn

@ramprasadn ramprasadn commented Apr 8, 2026

Copy link
Copy Markdown
Collaborator

NXF_SINGULARITY_NEW_PID_NAMESPACE cannot be set in nextflow.config. Environment variables like NXF_* are read by Nextflow during startup, before the configuration files are parsed. By the time nextflow.config is processed, it's too late to affect these settings.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@nf-core-bot

nf-core-bot commented Apr 8, 2026

Copy link
Copy Markdown
Member

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions

github-actions Bot commented Apr 8, 2026 •
edited
Loading

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f790998

+| ✅ 244 tests passed       |+
#| ❔   7 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
    _
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: hisat2

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-04-08 12:33:02

@ramprasadn ramprasadn marked this pull request as ready for review April 8, 2026 13:30
@ramprasadn ramprasadn merged commit 5912e48 into release300 Apr 8, 2026
85 of 87 checks passed
@ramprasadn ramprasadn deleted the removenxf branch May 18, 2026 12:23
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@ramprasadn @nf-core-bot