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Commits on Mar 12, 2024

• fixed bug in determining filenames for merge run

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  jhawkey

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Commits on Apr 21, 2021

• Update README.md to match new repo url

  

  scwatts

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Commits on Apr 20, 2021

• Set version req for jdk to major release only

  

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• Increase max queue size for job HPC schedulers

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  scwatts

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• Improve regex for read matching

  

  scwatts

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• Increase default walltime for some tasks

  

  scwatts

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• Update qos/partition choice for new max walltimes

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Commits on Mar 31, 2021

• Rollback libtbb to be compatible with bowtie2

  

  scwatts

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• Improve reference filetype detection

  

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Commits on Jan 1, 2021

• Update README.md

  

  scwatts

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• Remove unused test data

  

  scwatts

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Commits on Dec 14, 2020

• Use 'rd' job name prefix rather than 'rr'

  

  scwatts

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• Update test data

  

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• Force passing isolates w no SNPs in allele matrix

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Commits on Dec 1, 2020

• Update conda package list

  

  scwatts

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• Note version of NF for jobname rename

  

  scwatts

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• Use "final" DSL version, migrate depreciated code

  

  scwatts

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• Improve mapped, unmapped read splitting

  

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• Update test data

  

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Commits on Oct 19, 2020

• Fix job resubmission

  

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Commits on Sep 15, 2020

• Improve coding cons output; add strand

  

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Commits on Aug 18, 2020

• Add missing f-string syntax for compare_data.py

  

  scwatts

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• Use correct delimiter for merge run SNP sites

  

  scwatts

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• Update filenames in merge data validator

  

  scwatts

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• Update README.md

  

  scwatts

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• Update TODOs

  

  scwatts

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• Minor changes to nextflow.config

  

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• Renaming previous_run_dir to existing_run_dir

  

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• Update TODOs

  

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• Add new test data

  

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• Update end-to-end test comparison script

  

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• Update unit and functional tests

  

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• Fix ingroup calculation; catch failed records

  

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• Set correct file ext for gene depth/cov

  

  scwatts

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• Update TODOs

  

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