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Varlociraptor integration #1940

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famosab
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@famosab famosab commented Jul 15, 2025 •
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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/sarek 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>).
  • 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).

Followup to https://github.com/nf-core/sarek/pull/1154/files

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github-actions bot commented Jul 15, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 917ea0e

+| ✅ 226 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-19 13:50:09

nvnieuwk
nvnieuwk reviewed Jul 18, 2025
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nvnieuwk
nvnieuwk reviewed Jul 18, 2025
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nvnieuwk
nvnieuwk reviewed Jul 18, 2025
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@famosab famosab mentioned this pull request Jul 21, 2025
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famosab
famosab commented Jul 21, 2025
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maxulysse
maxulysse reviewed Jul 22, 2025
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@famosab famosab marked this pull request as ready for review July 25, 2025 08:53
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famosab commented Jul 25, 2025 

nextflow run . -profile test,singularity,variantcalling_channels --outdir testing --step variant_calling --tools strelka,varlociraptor --input tests/csv/3.0/recalibrated_germline.csv -dump-channels

nextflow run . -profile test,singularity,variantcalling_channels --outdir testing --step variant_calling --tools strelka,varlociraptor --input tests/csv/3.0/recalibrated.csv -dump-channels

nextflow run . -profile test,singularity,variantcalling_channels --outdir testing --step variant_calling --tools mutect2,varlociraptor --input tests/csv/3.0/recalibrated_somatic.csv -dump-channels

For testing!

FriederikeHanssen
FriederikeHanssen reviewed Jul 28, 2025
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conf/modules/post_variant_calling.config
Comment on lines +87 to +225
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_GERMLINE:SORT_CALLED_CHUNKS|NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_TUMOR_ONLY:SORT_CALLED_CHUNKS' {
ext.prefix = { "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" }
ext.args = { '--output-type z --write-index=tbi' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_GERMLINE:MERGE_CALLED_CHUNKS|NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_TUMOR_ONLY:MERGE_CALLED_CHUNKS' {
ext.prefix = { "${meta.id}.${meta.variantcaller}.varlociraptor" }
ext.args = { '--allow-overlaps --output-type z --write-index=tbi' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/" },
]
}

//
// VCF_VARLOCIRAPTOR_SOMATIC MODULES
//
withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:ALIGNMENTPROPERTIES_NORMAL' {
ext.prefix = { "${meta.normal_id}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:VCFSPLIT_NORMAL' {
ext.prefix = { "${meta.normal_id}.${meta.variantcaller}.split" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:PREPROCESS_NORMAL' {
ext.prefix = { "${meta.normal_id}.${meta.variantcaller}.preprocess.${meta.chunk}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.normal_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:ALIGNMENTPROPERTIES_TUMOR' {
ext.prefix = { "${meta.tumor_id}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:VCFSPLIT_TUMOR' {
ext.prefix = { "${meta.tumor_id}.${meta.variantcaller}.split" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:PREPROCESS_TUMOR' {
ext.prefix = { "${meta.tumor_id}.${meta.variantcaller}.preprocess.${meta.chunk}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.tumor_id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:VARLOCIRAPTOR_CALLVARIANTS' {
ext.prefix = { "${meta.id}.${meta.variantcaller}.call.${meta.chunk}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:SORT_CALLED_CHUNKS' {
ext.prefix = { "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" }
ext.args = { '--output-type z --write-index=tbi' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
]
}

withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:VCF_VARLOCIRAPTOR_SOMATIC:MERGE_CALLED_CHUNKS' {
ext.prefix = { "${meta.id}.${meta.variantcaller}.varlociraptor" }
ext.args = { '--allow-overlaps --output-type z --write-index=tbi' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/varlociraptor/" },
]
}
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let's move this to it's own file maybe

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Smart idea, I'm all for it

@famosab famosab added this to the 3.6 milestone Jul 28, 2025
maxulysse
maxulysse reviewed Aug 19, 2025
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CHANGELOG.md
Comment on lines 181 to +186
### Parameters

| Params | Status |
| ------ | ------ |
| Params | Status |
| ------------------------------ | ------ |
| `--varlocriator_scenario_file` | New |
| `--varlocriator_chunk_size` | New |
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Why do we have 2 parameters section?

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