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Commits on May 6, 2021

• limit host removal memory

  jts

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  b6d4d46

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Commits on Apr 13, 2021

• update README

  jts

  committed
  6ba6dae

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• update README

  jts

  committed
  71430ce

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• remove nanopore description, point to upstream

  jts

  committed
  80de957

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• updates to README

  jts

  committed
  0719248

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• fix link

  jts

  committed
  00a07de

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• update documentation to describe changes from base COG-UK version

  jts

  committed
  2a14506

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Commits on Mar 30, 2021

• add bcftools to environment

  jts

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  7ba2b17

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• add freebayes to environment

  jts

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  0a735e0

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Commits on Mar 6, 2021

• re-add variant output channel so vcf is exported

  jts

  committed
  be26bae

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• switch pipeline from ivar to freebayes

  jts

  committed
  a9a6515

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• rewrote freebayes pipeline to probably handle MNPs/multiallelics, better integration into pipeline

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  5bc14b6

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Commits on Mar 3, 2021

• remove assertion

  jts

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  7b92559

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• better handling of multi-allelic indels

  jts

  committed
  7453961

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Commits on Feb 4, 2021

• do not filter freebayes calls by variant quality

  jts

  committed
  5896555

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• fully functional version of the pipeline for initial tests

  jts

  committed
  61e2b8c

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Commits on Feb 1, 2021

• cleaner implementation, write a single variants file then split using awk

  jts

  committed
  6cc7aab

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• basic freebayes pipeline working alongside ivar

  jts

  committed
  0fdee60

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• fix assertion in host filter when empty files are input

  jts

  committed
  2f70310

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Commits on Nov 9, 2020

• remove CLIMB-specific modules/calls

  jts

  committed
  78b9cf9

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• update to ivar 1.3, add option for amplicon filtering

  jts

  committed
  725b9d7

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Commits on Sep 9, 2020

• restrict short adapter matches to the suffix of the read

  jts

  committed
  d4470ff

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Commits on Sep 8, 2020

• lower required match length for adapter check

  jts

  committed
  386f1a2

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Commits on Sep 4, 2020

• fix samtools/pysam version in environment

  jts

  committed
  6ffd46e

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• add step for filtering residual adapters missed by trimming

  jts

  committed
  4b1d956

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Commits on Sep 3, 2020

• increase minimum read length after trimming

  jts

  committed
  00a8e26

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• update ivar to 1.2.3

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  committed
  3542a2c

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Commits on Jul 14, 2020

• limit host removal cpus

  

  jts

  authored and

  mlaszloffy

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  4ee5fa3

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• synchronize host removal with SIGNAL

  

  jts

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  mlaszloffy

  committed
  d93579a

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• move host filter to within workflow

  

  jts

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  mlaszloffy

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  9038598

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• remove hardcoded paths

  

  jts

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  mlaszloffy

  committed
  99d0f35

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• add basic host filter step

  

  jts

  authored and

  mlaszloffy

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  6c68916

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