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Upd subsample#296

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LouisLeNezet wants to merge 4 commits into
nf-core:devfrom
LouisLeNezet:upd_subsample
Open

Upd subsample#296
LouisLeNezet wants to merge 4 commits into
nf-core:devfrom
LouisLeNezet:upd_subsample

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@LouisLeNezet

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Update subsampling subworkflow to use samtools/coverage.
This reduce quite a lot the file size compared to samtools/depth for full genome (x10Gb) and should also be faster.
The drawback is that you need to provide the region min and max when dealing with just part of chromosomes (as in the unit-test).

  • 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 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).

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