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Add auto detection of chr prefix and auto fixing #20

Merged
merged 18 commits into from
Mar 29, 2024
Merged

Add auto detection of chr prefix and auto fixing #20

merged 18 commits into from
Mar 29, 2024

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LouisLeNezet
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@LouisLeNezet LouisLeNezet commented Mar 22, 2024 •
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Add autodetection of contigs in vcf file and compare them to the fasta file.
Allow renaming of the chr prefix.

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/phaseimpute branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@LouisLeNezet LouisLeNezet self-assigned this Mar 24, 2024
@LouisLeNezet LouisLeNezet added the enhancement New feature or request label Mar 24, 2024
@LouisLeNezet LouisLeNezet linked an issue Mar 24, 2024 that may be closed by this pull request
Renaming chromosome automatically #7
Closed
@LouisLeNezet LouisLeNezet linked an issue Mar 27, 2024 that may be closed by this pull request
Error: Panel index file requirement - Invalid filename format and missing file extension #21
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@LouisLeNezet LouisLeNezet removed a link to an issue Mar 27, 2024
Error: Panel index file requirement - Invalid filename format and missing file extension #21
Closed
atrigila
atrigila requested changes Mar 27, 2024
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LouisLeNezet and others added 2 commits March 29, 2024 09:46
@LouisLeNezet @atrigila
Update nextflow_schema.json
8b8dd92 
Co-authored-by: Anabella Trigila <[email protected]>
@LouisLeNezet @atrigila
Update CHANGELOG.md
27e10a2 
Co-authored-by: Anabella Trigila <[email protected]>
atrigila
atrigila approved these changes Mar 29, 2024
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Great job! 🎉

@LouisLeNezet LouisLeNezet merged commit 3fbfb87 into nf-core:dev Mar 29, 2024
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atrigila pushed a commit to atrigila/phaseimpute that referenced this pull request Apr 10, 2024
@LouisLeNezet
Merge pull request nf-core#20 from LouisLeNezet/auto_chr_rename
b7f9332 
Add auto detection of chr prefix and auto fixing
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Apr 24, 2024
@LouisLeNezet LouisLeNezet deleted the auto_chr_rename branch May 30, 2024 10:16
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@atrigila atrigila atrigila approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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@LouisLeNezet LouisLeNezet

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enhancement New feature or request
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Renaming chromosome automatically
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@LouisLeNezet @atrigila