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[dup] Add support for variant scoring by MIVMIR, GICAM models - #849

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variant-scoring-by-mivmir-gicam
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[dup] Add support for variant scoring by MIVMIR, GICAM models#849
torbjorgen wants to merge 1 commit into
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variant-scoring-by-mivmir-gicam

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@torbjorgen

@torbjorgen torbjorgen commented May 19, 2026

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Duplicate of #812 to test CICD with Sentieon licence.

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nf-core-bot commented May 19, 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.

@torbjorgen torbjorgen changed the title Add support for variant scoring by MIVMIR, GICAM models [dup] Add support for variant scoring by MIVMIR, GICAM models May 19, 2026
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fd71265

+| ✅ 251 tests passed       |+
#| ❔   6 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  10 tests had warnings |!
Details

❗ 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

❔ 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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-26 11:41:49

@torbjorgen
torbjorgen force-pushed the variant-scoring-by-mivmir-gicam branch 2 times, most recently from 9916853 to 7fa6051 Compare May 27, 2026 11:14
@torbjorgen
Add support for variant scoring by MIVMIR, GICAM models
fd71265 
Signed-off-by: Tor Björgen <tor.bjorgen@scilifelab.se>
@torbjorgen
torbjorgen force-pushed the variant-scoring-by-mivmir-gicam branch from 7fa6051 to fd71265 Compare June 26, 2026 11:37
@ramprasadn ramprasadn mentioned this pull request Jun 27, 2026
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@ramprasadn ramprasadn linked an issue Jul 4, 2026 that may be closed by this pull request
Add MIVMIR, GICAM models for SNV ranking #816
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Add MIVMIR, GICAM models for SNV ranking

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@torbjorgen @nf-core-bot @fellen31