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Commits on Aug 8, 2025

• Merge pull request #59 from pughlab/dev

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• update to v0.9.17

  

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  483ab4a

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Commits on Aug 6, 2025

• added picard QC step

  

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  d02d327

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• added stage for adapter trimming

  

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  9baa0d1

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• updated filepaths

  

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  07693de

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• removed non-default site lists

  

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  a1ba549

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• removed broken paths

  

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  9ff7b00

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• bugfix

  

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  d7291ee

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• bugfix

  

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  1ba47b0

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• bugfix

  

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  26f8012

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Commits on Jul 15, 2025

• fixed dinucleotide profiling for short frags

  

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  67d7c04

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Commits on Jul 11, 2025

• fixed an error in tumour-only cleanup

  

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  b00ed98

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Commits on Jul 10, 2025

• Merge pull request #58 from pughlab/dev

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• updated version #

  

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• Merge pull request #57 from pughlab/dev

  Show description for 66f6ecb
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• minor updates

  

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  0d1430b

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• minor updates

  

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  245336f

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• added UMI extraction for capHLA

  

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  0f96b46

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• minor bug fixes

  

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  da37516

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• changed default version for use on H4H

  

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  8323f74

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Commits on Jun 13, 2025

• updated default tool versions

  

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• added option to downsample

  

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  12c67eb

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Commits on Jun 10, 2025

• incorporated new genotype concordance method

  

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  a1ad4c9

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• incorporated new genotype concordance method

  

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  0d60209

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• increased variant specificity to remove duplciates

  

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  4165949

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• pulls bwa version from config

  

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  77520bf

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• modified cluster partition requirements

  

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  09c35d2

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• added VarScan2seqz function

  

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  7472db7

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• removed default R version

  

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  c9a41db

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• updates to intervals processing

  

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  ea6009d

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• allow n_cpu specification for get_coverage

  

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Commits on Apr 2, 2025

• Merge pull request #55 from pughlab/dev

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• PughLab pipeline-suite (version 0.9.15)

  

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  a46412c

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• added functionality for v1.3

  

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  edfa5a7

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• added argument sequencing type

  

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