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Add QUILT method #26

Merged
merged 36 commits into from
Apr 20, 2024
Merged

Add QUILT method #26

merged 36 commits into from
Apr 20, 2024

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atrigila
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@atrigila atrigila commented Apr 10, 2024 •
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Closes #24
First implementation of QUILT in phaseimpute.
Future improvements will include:

  • Using optional files (genetic map file, phasefile, posfiles). This requires modification of general params used in the pipeline.

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).

@atrigila atrigila requested a review from LouisLeNezet April 10, 2024 15:16
@atrigila atrigila self-assigned this Apr 10, 2024
LouisLeNezet
LouisLeNezet requested changes Apr 10, 2024
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subworkflows/local/quilt_subworkflows/concatenate_vcf.nf Outdated Show resolved Hide resolved
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subworkflows/local/quilt_subworkflows/make_chunks.nf Outdated Show resolved Hide resolved
@atrigila atrigila requested a review from LouisLeNezet April 18, 2024 22:10
LouisLeNezet
LouisLeNezet requested changes Apr 19, 2024
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@atrigila atrigila requested a review from LouisLeNezet April 19, 2024 13:44
@LouisLeNezet
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Nicely done @atrigila !
Just a little comment on index creation, but everything ready to go 😉

@atrigila atrigila merged commit 7addfc7 into nf-core:dev Apr 20, 2024
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@LouisLeNezet LouisLeNezet added the enhancement New feature or request label Apr 24, 2024
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Apr 24, 2024
@atrigila atrigila deleted the add_quilt_4 branch May 6, 2024 12:19
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@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

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@atrigila atrigila

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enhancement New feature or request
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Add quilt to the pipeline
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@atrigila @LouisLeNezet