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Commits on Sep 25, 2024

• updating slurm job resources definitions

  BenjaminJPerry

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Commits on Aug 7, 2024

• updating paths to 2024_illumina_sequencing_e

  BenjaminJPerry

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  0822b56

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Commits on Mar 21, 2024

• Merge pull request #46 from BenjaminJPerry/master

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  afmcc

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  59560b1

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• refactoring 2023_illumina_sequencing_c -> 2024_illumina_sequencing_d

  BenjaminJPerry

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  3eb6713

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Commits on Mar 20, 2024

• minor tweak to autostart example and help

  afmcc

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Commits on Mar 1, 2024

• remove two obsolete scripts

  afmcc

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  d88c4de

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• refactor dump of GBS tables thats done before keyfile import, to use gquery rather than psql

  afmcc

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Commits on Feb 29, 2024

• refactor GBS extract for warehouse, to use gquery rather than psql

  afmcc

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Commits on Feb 20, 2024

• repo tidy

  afmcc

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• repo tidy

  afmcc

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  d5ca6e0

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• repo tidy; added scripts from gbs_utils repo

  afmcc

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Commits on Feb 9, 2024

• remove importOrUpdateKeyfile.sh ; add more sample sheet checking

  afmcc

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  603d499

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Commits on Nov 14, 2023

• make stats import more specific

  afmcc

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  dd0e240

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Commits on Oct 2, 2023

• roll over to new filesystem root for uploads and processing

  afmcc

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Commits on Sep 29, 2023

• Merge pull request #42 from AgResearch/doddsk-patch-5

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  afmcc

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  4a8eff7

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• Merge pull request #39 from BenjaminJPerry/patch-1

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  afmcc

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  88ddf69

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• Merge pull request #40 from BenjaminJPerry/master-1

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  afmcc

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  007b616

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• Update run_kgd.R

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  doddsk

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Commits on Sep 15, 2023

• clarify error message and feed back gquery code used for getting what cohorts there are

  afmcc

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  b0d94d7

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Commits on Aug 28, 2023

• utility for analysing and patching PstI cut site (not currently used, related to previous issues with PstI cutsite sequencing errors)

  afmcc

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Commits on Aug 25, 2023

• adding andrewsa, henryh, frenchm, hicklandm to auto-emails

  BenjaminJPerry

  authored
  4c1703d

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• Adding andrewsa, henryh, frenchm, hicklandm to auto-emails

  BenjaminJPerry

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  dde2ce9

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Commits on Aug 7, 2023

• utility to scrape fastq for GBS barcodes

  afmcc

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Commits on Jul 28, 2023

• test integrity of gbsx demultiplex results

  afmcc

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Commits on Jul 26, 2023

• adding --interactive to multiqc call in ag_gbs_qc_prism.sh

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  BenjaminJPerry

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  eb77317

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Commits on Jul 10, 2023

• example of batch script for running demultiplex and KGD with minimal dependencies

  afmcc

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  cdf1771

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• making a minimal q/c target to speed up processing

  BenjaminJPerry

  committed
  973ecdf

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Commits on Jun 27, 2023

• fix return code from fasta_demultiplex

  afmcc

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Commits on Jun 26, 2023

• switching to sequencing_b and passing paths to gquery

  afmcc

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Commits on Jun 24, 2023

• path names

  afmcc

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  dcc8420

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Commits on May 17, 2023

• added script to redo genotyping for old flowcells using latest KGD, and import results to database

  afmcc

  committed
  b21a5b6

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• patch for annoying broken pipe error when piping reconcile_contaminants.py to e.g. head -30

  afmcc

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Commits on May 5, 2023

• remove obsolete doc

  afmcc

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  0224b85

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• Update beta-binomial-adjustment.md

  afmcc

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  d022569

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• Update beta-binomial-adjustment.md

  afmcc

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