Code

Nextalign rebased index seq pr#562

Code

Merged

huddlej merged 38 commits intomasternextstrain/ncov:masterfrom nextalign-rebased-index-seq-prnextstrain/ncov:nextalign-rebased-index-seq-prCopy head branch name to clipboardFeb 23, 2021

+698-326

Commits

Commits on Feb 23, 2021

• add nextalign option

  

  rneher

  authored and

  huddlej

  committed
  bb0e90d

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• remove filter rules

  

  rneher

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  huddlej

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  b4a2839

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• re-allow opt-in diagnostics & remove unused code

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  jameshadfield

  authored and

  huddlej

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  ac2f63c

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• extend filter time limit

  

  rneher

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  huddlej

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  f80b455

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• add translations

  

  rneher

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  c14f832

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• add mutation_summary rule and script

  

  rneher

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  a4244a3

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• fix paths

  

  rneher

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  d259902

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• add annotation

  

  rneher

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  50ceffa

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• fix argument name

  

  rneher

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  b30f876

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• add alignment for build

  

  rneher

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  5bb46bf

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• fix wild card

  

  rneher

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  d4ca026

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• add explicit translation script

  

  rneher

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  9816596

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• fix missing output error when origin is null

  

  rneher

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  295309f

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• fix wildcard/basename

  

  rneher

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  21bf857

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• don't restart failed jobs. we don't have stochastic failures anymore

  

  rneher

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  1d06242

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• fix script name

  

  rneher

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  773bbd4

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• increase memory req for proximity rule

  

  rneher

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  b484186

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• reenable restarts, mainly for oom reasons

  

  rneher

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  ad7b386

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• add index

  

  rneher

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  040f675

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• fix

  

  rneher

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  2a27d6b

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• use function to determine unified alignment

  

  rneher

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  c1beeec

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• Fix snakemake errors for pipelines without nextalign

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  jameshadfield

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  huddlej

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  0f0d73b

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• calculate priorities sequentially

  

  rneher

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  huddlej

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  5584c88

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• fix

  

  rneher

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  e58d1f9

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• fix

  

  rneher

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  4dee5d7

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• split priorities into proximities and priorities

  

  rneher

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  8446693

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• remove metadata from proximity

  

  rneher

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  fc0e7dd

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• fix import

  

  rneher

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  9adefea

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• fix

  

  rneher

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  ac30ca0

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• remove accidentally committed file, upload mutation summary

  

  rneher

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  b83c75c

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• Update conda environments for new rules

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  huddlej

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  211aa0d

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• Request more CPUs and less memory for alignment on rhino cluster

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  huddlej

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• adjust docstrings

  

  rneher

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  161fc55

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• adjust resources

  

  rneher

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  7453c71

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• Parameterize chunk size for proximity score calculations

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  huddlej

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  4578781

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• Specify memory resources for higher-memory rules

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  huddlej

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  27b8856

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• Update Hutch-based cluster job submission commands

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  huddlej

  committed
  b542bee

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• Only install nextalign for nextstrain builds

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  huddlej

  committed
  4c2cb3f

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