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Commits on Sep 25, 2024

• updating slurm job resources definitions

  BenjaminJPerry

  authored
  dc5a71a

Commits on Aug 7, 2024

• updating paths to 2024_illumina_sequencing_e

  BenjaminJPerry

  authored
  0822b56

Commits on Mar 21, 2024

• Merge pull request #46 from BenjaminJPerry/master

  Show description for 59560b1
  afmcc

  authored
  59560b1

• refactoring 2023_illumina_sequencing_c -> 2024_illumina_sequencing_d

  BenjaminJPerry

  authored
  3eb6713

Commits on Mar 20, 2024

• minor tweak to autostart example and help

  afmcc

  committed
  ca3c260

Commits on Mar 1, 2024

• remove two obsolete scripts

  afmcc

  committed
  d88c4de

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

  afmcc

  committed
  51e25d9

Commits on Feb 29, 2024

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

  afmcc

  committed
  232424f

Commits on Feb 20, 2024

• repo tidy

  afmcc

  committed
  0d4092a

• repo tidy

  afmcc

  committed
  d5ca6e0

• repo tidy; added scripts from gbs_utils repo

  afmcc

  committed
  bba8d3d

Commits on Feb 9, 2024

• remove importOrUpdateKeyfile.sh ; add more sample sheet checking

  afmcc

  committed
  603d499

Commits on Nov 14, 2023

• make stats import more specific

  afmcc

  committed
  dd0e240

Commits on Oct 2, 2023

• roll over to new filesystem root for uploads and processing

  afmcc

  committed
  257e149

Commits on Sep 29, 2023

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

  Show description for 4a8eff7
  afmcc

  authored
  4a8eff7

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

  Show description for 88ddf69
  afmcc

  authored
  88ddf69

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

  Show description for 007b616
  afmcc

  authored
  007b616

• Update run_kgd.R

  Show description for 53dd930
  doddsk

  authored
  53dd930

Commits on Sep 15, 2023

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

  afmcc

  committed
  b0d94d7

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

  committed
  eb6cf53

Commits on Aug 25, 2023

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

  BenjaminJPerry

  authored
  4c1703d

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

  BenjaminJPerry

  authored
  dde2ce9

Commits on Aug 7, 2023

• utility to scrape fastq for GBS barcodes

  afmcc

  committed
  4b6f9ec

Commits on Jul 28, 2023

• test integrity of gbsx demultiplex results

  afmcc

  committed
  eee95c0

Commits on Jul 26, 2023

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

  Show description for eb77317
  BenjaminJPerry

  authored
  eb77317

Commits on Jul 10, 2023

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

  afmcc

  committed
  cdf1771

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

  BenjaminJPerry

  committed
  973ecdf

Commits on Jun 27, 2023

• fix return code from fasta_demultiplex

  afmcc

  committed
  90fbf2d

Commits on Jun 26, 2023

• switching to sequencing_b and passing paths to gquery

  afmcc

  committed
  6353da1

Commits on Jun 24, 2023

• path names

  afmcc

  committed
  dcc8420

Commits on May 17, 2023

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

  afmcc

  committed
  b21a5b6

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

  afmcc

  committed
  b0b4f0e

Commits on May 5, 2023

• remove obsolete doc

  afmcc

  committed
  0224b85

• Update beta-binomial-adjustment.md

  afmcc

  authored
  d022569

• Update beta-binomial-adjustment.md

  afmcc

  authored
  def5ef3

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