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Always run all SV callers #542

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merged 15 commits into from
Feb 13, 2025

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fellen31
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@fellen31 fellen31 commented Jan 21, 2025

This PR always runs all SV-callers. This changes the output files for sample, e.g.:

svs/sample/HG002_ONT_B/HG002_ONT_B_svs.vcf.gz

is replaced by:

svs/sample/HG002_ONT_B/HG002_ONT_B_severus_svs.vcf.gz
svs/sample/HG002_ONT_B/HG002_ONT_B_sniffles_svs.vcf.gz

In addition, add a hidden parameter --publish_unannotated_family_svs was added. This will output merged family calls per caller. This parameter has been added to the samplesheet_multisample_bam_ont test, and for example outputs the following family files:

                "svs/family/FAM/FAM_hificnv_cnvs.vcf.gz",
                "svs/family/FAM/FAM_hificnv_cnvs.vcf.gz.tbi",
                "svs/family/FAM/FAM_severus_svs.vcf.gz",
                "svs/family/FAM/FAM_severus_svs.vcf.gz.tbi",
                "svs/family/FAM/FAM_sniffles_svs.vcf.gz",
                "svs/family/FAM/FAM_sniffles_svs.vcf.gz.tbi",

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
  • 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).

@fellen31 fellen31 linked an issue Jan 21, 2025 that may be closed by this pull request
@fellen31 fellen31 marked this pull request as ready for review January 22, 2025 16:21
@fellen31 fellen31 requested a review from a team as a code owner January 22, 2025 16:21
@fellen31 fellen31 marked this pull request as draft January 24, 2025 14:07
@fellen31 fellen31 force-pushed the several-sv-callers branch 3 times, most recently from 35e2100 to 94f782e Compare February 10, 2025 14:41
@fellen31 fellen31 marked this pull request as ready for review February 10, 2025 15:01
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Looks good! Just a couple of questions

CHANGELOG.md Show resolved Hide resolved
nextflow_schema.json Show resolved Hide resolved
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@fellen31 fellen31 merged commit e0b41a4 into genomic-medicine-sweden:dev Feb 13, 2025
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@fellen31 fellen31 deleted the several-sv-callers branch February 13, 2025 06:43
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Possibility to run more than one SV-caller
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