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Add somalier subworkflow#878

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Add somalier subworkflow#878
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@peterpru

@peterpru peterpru commented Jun 11, 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 Jun 11, 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.

@peterpru peterpru self-assigned this Jun 11, 2026
@github-actions

github-actions Bot commented Jun 12, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 1e04dab

+| ✅ 242 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  11 tests had warnings |!
-| ❌   2 tests failed       |-
Details

❌ Test failures:

  • schema_params - Param run_somalier from nextflow config not found in nextflow_schema.json
  • schema_params - Param somalier_sites_vcf from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • container_configs - Could not generate container configuration files: Command 'nextflow inspect -format json /home/runner/work/raredisease/raredisease' returned non-zero error code '1':
    [red]>
    Error workflows/raredisease.nf:883:9: VCF_EXTRACT_RELATE_SOMALIER is not defined
    │ 883 | VCF_EXTRACT_RELATE_SOMALIER(
    ╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error workflows/raredisease.nf:891:31: VCF_EXTRACT_RELATE_SOMALIER is not defined
│ 891 | ch_somalier_publish = VCF_EXTRACT_RELATE_SOMALIER.out.html
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error workflows/raredisease.nf:892:18: VCF_EXTRACT_RELATE_SOMALIER is not defined
│ 892 | .mix(VCF_EXTRACT_RELATE_SOMALIER.out.pairs_tsv)
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error workflows/raredisease.nf:893:18: VCF_EXTRACT_RELATE_SOMALIER is not defined
│ 893 | .mix(VCF_EXTRACT_RELATE_SOMALIER.out.samples_tsv)
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^

ERROR ~ Script compilation failed

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • 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 passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-12 07:39:47

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