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Adding gvcf #137

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Adding gvcf #137

wants to merge 4 commits into from

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maxulysse
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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/rnavar branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@maxulysse
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@nf-core-bot fix linting pretty please

@MathieuCharlesINRAE
gvcf processing included in the base nfcore/haplotypecaller rule. whe…
7dc07ad 
…n --generate_gvcf is enable, will output only the gvcf not the vcf and the gvcf. fix for --skip_baserecalibration that was skipping recalibration but also the calling
@maxulysse
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@MathieuCharlesINRAE thanks a lot, I'll try solving the merge conflicts

@maxulysse
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ok, so I tried merging the merge conflicts in #137, and I'm giving up as it's way too out of date, but I'll copy over the changes in #138, and will merge that ASAP

@maxulysse maxulysse closed this May 27, 2024
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@maxulysse @MathieuCharlesINRAE