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Add info in sample_id_map into the main samplesheet as an optional customer_id column - #946

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issue861
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Add info in sample_id_map into the main samplesheet as an optional customer_id column#946
ramprasadn wants to merge 8 commits into
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issue861

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@ramprasadn

@ramprasadn ramprasadn commented Jul 29, 2026

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Closes #861

Replaces the separate --sample_id_map CSV (mapping internal_id → customer_id) with an optional customer_id column directly on the main --input samplesheet, so customer/external IDs can be supplied alongside each sample instead of maintaining a second file.

  • Add customer_id as an optional, meta-tagged column to assets/schema_input.json (same pattern as paternal_id/maternal_id); remove assets/sample_id_map.json
  • Remove the --sample_id_map parameter
  • Simplify call_sv_MT and generate_cytosure_files: both now read meta.customer_id coming from the samplesheet directly, instead of joining a separate ch_sample_id_map channel
  • generate_cytosure_files now gates VCF header renaming per-sample (meta.custid != meta.id) instead of on a pipeline-wide flag, so runs that don't use customer_id do not trigger reheader

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).

@github-actions

github-actions Bot commented Jul 29, 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: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@ramprasadn

ramprasadn commented Jul 29, 2026

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@nf-core-bot fix linting

@github-actions

github-actions Bot commented Jul 29, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34651d7

+| ✅ 256 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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 4.0.3
  • Run at 2026-07-30 09:15:28

@github-actions

github-actions Bot commented Jul 29, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 22/25

See the full run for details.

@ramprasadn
ramprasadn marked this pull request as ready for review July 30, 2026 07:27
@ramprasadn ramprasadn closed this Jul 30, 2026
@ramprasadn ramprasadn reopened this Jul 30, 2026
@ramprasadn ramprasadn closed this Jul 30, 2026
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@ramprasadn @nf-core-bot