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selectROI.py removed as samtools now can do it better and in parallel#243

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maxulysse merged 3 commits intonf-core:devfrom
szilvajuhos:roi
Jul 16, 2020
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selectROI.py removed as samtools now can do it better and in parallel#243
maxulysse merged 3 commits intonf-core:devfrom
szilvajuhos:roi

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@szilvajuhos
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@szilvajuhos szilvajuhos commented Jul 16, 2020

nf-core/sarek pull request

PR checklist

  • We do not need this obsolete script anymore as samtools can do it better and faster
  • Documentation in docs is updated
  • CHANGELOG.md is updated

@szilvajuhos szilvajuhos requested a review from maxulysse as a code owner July 16, 2020 06:54
@maxulysse
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Do we have a samtools process to do that?

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samtools view -@48 -L target.bed -o targeted.bam input.bam can do that

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ok, we'll think of a process to do that in DSL2 then

Comment thread CHANGELOG.md Outdated
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sure, sorry for the expandtab

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sure, sorry for the expandtab

no worry, there was just a markdown linting error

@maxulysse maxulysse merged commit 1c9454c into nf-core:dev Jul 16, 2020
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2 participants