nf-core

There is a newer version of the record available.

Published February 13, 2025 | Version 2.3.0
Software Open

nf-core/raredisease: 2.3.0 - Getafix

Authors/Creators

  • 1. Scilifelab
  • 2. Clinical Genomics Lund
  • 3. University of Gothenburg
  • 4. Dep. of Molecular Medicine (MOMA)
  • 5. Clinical Genomics
  • 6. Karolinska Institutet Library
  • 7. @Clinical-Genomics-Lund
  • 8. Oligonovahub
  • 9. Linköping university hospital
  • 10. Lund University Hospital
  • 11. @mendelics
  • 12. @seqeralabs
  • 13. Robert Bosch GmbH

Description

What's Changed

  • Bumpversion 2.2.0->2.3.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/610
  • Add option to analyse only mitochondria by @ramprasadn in https://github.com/nf-core/raredisease/pull/608
  • 5% frequency threshold for mitochondrial clinical vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/616
  • allow vep 112 by @jemten in https://github.com/nf-core/raredisease/pull/617
  • Minor fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/618
  • update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/619
  • Change output file prefix for upd and chromograph by @ramprasadn in https://github.com/nf-core/raredisease/pull/620
  • Invoke rhocallviz subworkflow only once per sample. by @ramprasadn in https://github.com/nf-core/raredisease/pull/621
  • Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/623
  • Fix channel declaration error in the cadd subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/624
  • Update genmod and multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/625
  • template update 3.0.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/629
  • Important! Template update for nf-core/tools v3.0.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/628
  • Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/630
  • ensure string comparison by @jemten in https://github.com/nf-core/raredisease/pull/632
  • add bait regions to deepvariant for WES by @ramprasadn in https://github.com/nf-core/raredisease/pull/633
  • Merge germlinecnvcaller output by @ramprasadn in https://github.com/nf-core/raredisease/pull/635
  • Raredisease: Add fastp output to multiqc by @peterpru in https://github.com/nf-core/raredisease/pull/637
  • Fix fastqc samplenames in multiqc report by @ramprasadn in https://github.com/nf-core/raredisease/pull/638
  • Vep update to 113 by @ramprasadn in https://github.com/nf-core/raredisease/pull/639
  • Use target bed files as regions instead of bait intervals for SNV calling in WES samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/636
  • Upd fix by @jemten in https://github.com/nf-core/raredisease/pull/643
  • Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/646
  • Add option to restrict analysis to specific contigs by @ramprasadn in https://github.com/nf-core/raredisease/pull/644
  • add fastp and ngsbits to multiqc input by @peterpru in https://github.com/nf-core/raredisease/pull/647
  • Fix tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/648
  • patch vep 110 by @ramprasadn in https://github.com/nf-core/raredisease/pull/649
  • Sync v3.1.1 of nf-core template by @ramprasadn in https://github.com/nf-core/raredisease/pull/655
  • Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/654
  • Remove suffixes sample name in repeat call vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/657
  • Update module MultiQC to version 1.26 by @peterpru in https://github.com/nf-core/raredisease/pull/660
  • padding bed file by @jemten in https://github.com/nf-core/raredisease/pull/658
  • Fix sex by @jemten in https://github.com/nf-core/raredisease/pull/659
  • Pre release PR1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/664
  • set meta.id for some input files by @jemten in https://github.com/nf-core/raredisease/pull/661
  • Add haplocheck to multiqc by @fevac in https://github.com/nf-core/raredisease/pull/662
  • Pre release PR2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/665
  • Fix download tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/667
  • Important! Template update for nf-core/tools v3.1.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/668
  • Review suggestions on v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/669
  • Template update v320 by @ramprasadn in https://github.com/nf-core/raredisease/pull/671
  • Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/670
  • update haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/672
  • Keep only SVs that PASS the filter by @ramprasadn in https://github.com/nf-core/raredisease/pull/673
  • Update versions by @ramprasadn in https://github.com/nf-core/raredisease/pull/674
  • Add option to skip haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/675
  • Release v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/666

New Contributors

  • @fevac made their first contribution in https://github.com/nf-core/raredisease/pull/662

Full Changelog: https://github.com/nf-core/raredisease/compare/2.2.0...2.3.0

Files

nf-core/raredisease-2.3.0.zip

Files (3.3 MB)

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md5:dc3d988d4355e4ddb1b60d07993c618b
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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/raredisease/tree/2.3.0 (URL)

Software

Repository URL
https://github.com/nf-core/raredisease