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Merged
merged 34 commits into from
Jun 16, 2025
Merged

Template update to 3.3.1 #707

merged 34 commits into from
Jun 16, 2025

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ramprasadn
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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_one_sample,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).

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github-actions bot commented Jun 4, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9165128

+| ✅ 219 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  28 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in 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 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 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 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 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 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
  • local_component_structure - annotate_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_cytosure_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - scatter_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variant_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - subsample_mt.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mt_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - qc_bam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_genome_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - call_snv.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rank_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - annotate_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - gens.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - generate_clinical_set.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ 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 passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-16 08:46:22

ramprasadn added 27 commits June 4, 2025 10:13
@ramprasadn
update version
12327be
@ramprasadn
update version
ac77cf3
@ramprasadn
stub run
cbd95fd
@ramprasadn
fix pre-commit fail
f3dd9f1
@ramprasadn
add stub
33310b2
@ramprasadn
add a clean up step
561d286
@ramprasadn
add tools to skip
8a36968
@ramprasadn
add more skips
eb1b859
@ramprasadn
turn off test in CI
ba8447f
@ramprasadn
option to turn off eklipse
fb7cea1
@ramprasadn
Merge branch 'template-update' of github.com:nf-core/raredisease into…
9aa69ef 
… template-update
@ramprasadn
fix conditionals
b004775
@ramprasadn
Merge branch 'template-update' of github.com:nf-core/raredisease into…
c205be8 
… template-update
@ramprasadn
test
41b0404
@ramprasadn
pdiff
dd504c9
@ramprasadn
update configs
8d4f75c
@ramprasadn
pre-commit fix
cb85720
@ramprasadn
updatae snapshot for test & test bam
c215cd5
@ramprasadn
Merge branch 'template-update' of github.com:nf-core/raredisease into…
dbf32dd 
… template-update
@ramprasadn
update skips
da269e7
@ramprasadn
update skip_subworkflows
cb278bc
@ramprasadn
update skip_subworkflows
101e437
@ramprasadn
update skip_subworkflows again
cd0e098
@ramprasadn
update vep container
103a18a
@ramprasadn
set a vep image
7be2b98
@ramprasadn
remove sentieon
43e1cad
@ramprasadn
update configs
20aa9a7
@ramprasadn ramprasadn requested a review from maxulysse June 12, 2025 07:56
@ramprasadn ramprasadn marked this pull request as ready for review June 12, 2025 07:56
maxulysse
maxulysse reviewed Jun 16, 2025
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maxulysse
maxulysse reviewed Jun 16, 2025
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maxulysse
maxulysse reviewed Jun 16, 2025
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@ramprasadn ramprasadn merged commit d076745 into dev Jun 16, 2025
14 checks passed
@ramprasadn ramprasadn deleted the template-update branch June 25, 2025 08:52
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@maxulysse maxulysse maxulysse approved these changes

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@ramprasadn @maxulysse @nf-core-bot