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Migrate file publishing from publishDir to centralized output {} block - V#791

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ramprasadn merged 7 commits into
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outputblock5
Mar 19, 2026
Merged

Migrate file publishing from publishDir to centralized output {} block - V#791
ramprasadn merged 7 commits into
devfrom
outputblock5

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@ramprasadn

@ramprasadn ramprasadn commented Mar 18, 2026

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PR checklist

  • 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 Mar 18, 2026

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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 Mar 18, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 982da9d

+| ✅ 234 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 2026-03-18 21:10:41

@ramprasadn ramprasadn marked this pull request as ready for review March 18, 2026 21:29
@ramprasadn ramprasadn requested review from maxulysse March 18, 2026 21:43
maxulysse
maxulysse reviewed Mar 19, 2026
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Comment thread subworkflows/local/prepare_references/tests/main.nf.test
assert snapshot(workflow.out).match()
assertAll(
{ assert workflow.success },
{ assert snapshot(

@maxulysse maxulysse Mar 19, 2026

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I think you can simplify that:

https://github.com/nf-core/rnavar/blob/dev/subworkflows/local/prepare_genome/tests/main.nf.test#L78-L92

maxulysse
maxulysse approved these changes Mar 19, 2026
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@maxulysse maxulysse left a comment

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Minor comments on the tests, but ok for me to merge as is if you want/need to

@ramprasadn ramprasadn merged commit 470950f into dev Mar 19, 2026
16 checks passed
@ramprasadn ramprasadn deleted the outputblock5 branch March 30, 2026 18:47
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@ramprasadn @nf-core-bot @maxulysse