Sofia Stamouli
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97e48075c8
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Apply review suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-12-13 09:37:43 +01:00 |
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Sofia Stamouli
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a99f89af77
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2022-12-12 16:30:28 +01:00 |
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Sofia Stamouli
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bd5cd0a897
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Prettier
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2022-12-12 13:34:53 +01:00 |
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sofstam
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896a39e68d
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2022-12-12 13:19:59 +01:00 |
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Sofia Stamouli
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98f3ab9fd1
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Apply prettier
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2022-12-09 15:35:51 +01:00 |
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Sofia Stamouli
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a622dcaef0
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Delete one line
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2022-12-09 13:59:37 +01:00 |
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sofstam
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5373c58331
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Merge branch 'dev' into update_usage
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2022-12-09 13:05:42 +01:00 |
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sofstam
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97fbc2bceb
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Update usage.md
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2022-12-09 12:58:51 +01:00 |
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James A. Fellows Yates
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13c4f44ca6
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Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1
Important! Template update for nf-core/tools v2.7.1
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2022-12-09 12:58:28 +01:00 |
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sofstam
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f0846ef213
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Merge branch 'update_usage' of https://github.com/genomic-medicine-sweden/taxprofiler into update_usage
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2022-12-09 10:38:03 +01:00 |
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sofstam
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3af71d9c63
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Merge branch 'dev' into update_usage
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2022-12-09 10:35:12 +01:00 |
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James Fellows Yates
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dca0b86c78
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Fix versions
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2022-12-09 10:28:48 +01:00 |
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James Fellows Yates
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da3d2d96e6
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Fix linting
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2022-12-09 10:27:50 +01:00 |
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James Fellows Yates
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1ccd0a0767
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Merge branch 'dev' into nf-core-template-merge-2.7.1
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2022-12-09 10:16:17 +01:00 |
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nf-core-bot
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36f3b5723b
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Template update for nf-core/tools version 2.7.1
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2022-12-08 13:18:23 +00:00 |
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James A. Fellows Yates
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1687b43596
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Merge pull request #183 from nf-core/update-bracken-params
Update bracken so parameters come directly from database args
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2022-12-07 16:39:52 +01:00 |
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James Fellows Yates
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d8751787ac
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Update bracken so parameters come directly from database args
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2022-12-07 07:27:40 +01:00 |
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Sofia Stamouli
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50da3d3efb
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Merge branch 'nf-core:dev' into update_usage
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2022-12-06 17:13:17 +01:00 |
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James Fellows Yates
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3dba6405c5
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Sets correct default for --shortread_qc_mergepairs
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2022-12-06 11:47:16 +01:00 |
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Moritz E. Beber
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9064584356
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Merge pull request #180 from nf-core/rename-exclude-unmerged
refactor: change parameter exclude unmerged to include
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2022-12-05 10:53:32 +01:00 |
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Moritz E. Beber
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24e5bc5410
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refactor: use shorter and more explicit syntax
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2022-12-04 21:54:10 +01:00 |
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Moritz E. Beber
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b2088bcbb3
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docs: improve description of shortread_qc_includeunmerged
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2022-12-04 21:53:38 +01:00 |
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Moritz E. Beber
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4529e7e545
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refactor: change parameter exclude unmerged to include
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2022-12-04 21:36:12 +01:00 |
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James A. Fellows Yates
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7992edd181
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Merge pull request #181 from nf-core/sep-krakenuniq-test
Filter out Nanopore reads from Bracken
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2022-12-04 13:57:11 +01:00 |
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James Fellows Yates
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0a0dffa37c
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Try separating MALT
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2022-12-04 12:06:33 +01:00 |
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James Fellows Yates
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0dccfddc24
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Switch order back
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2022-12-03 21:38:25 +01:00 |
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James A. Fellows Yates
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cf8ad96771
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Update subworkflows/local/profiling.nf
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2022-12-02 15:09:08 +01:00 |
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James Fellows Yates
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ab42f6b662
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wteak message
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2022-12-02 12:49:00 +01:00 |
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James Fellows Yates
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a3cd188b1f
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Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test
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2022-12-02 12:48:18 +01:00 |
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James Fellows Yates
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de74e4f727
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Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md
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2022-12-02 12:47:14 +01:00 |
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Sofia Stamouli
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c56c6ea694
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Merge pull request #176 from nf-core/update_motus
Include NCBI taxid, read counts and mgc arguments in motus
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2022-12-02 12:18:58 +01:00 |
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Sofia Stamouli
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7e7299203c
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Set values to false
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2022-12-02 08:55:23 +01:00 |
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sofstam
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6d140c683a
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Merge branch 'dev' into update_motus
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2022-12-01 18:49:23 +01:00 |
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James A. Fellows Yates
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80c25008d0
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Merge pull request #177 from nf-core/sep-krakenuniq-test
Separate KrakenUniq test run
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2022-12-01 17:34:30 +01:00 |
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nf-core-bot
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410196c37b
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[automated] Fix linting with Prettier
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2022-12-01 14:33:34 +00:00 |
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sofstam
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4800a5f03e
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Update schema
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2022-12-01 14:23:40 +01:00 |
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James A. Fellows Yates
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a34b240dfc
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Merge pull request #174 from nf-core/malt-update
Update MALT
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2022-12-01 13:58:30 +01:00 |
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James Fellows Yates
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f960c14caf
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Fix typos
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2022-12-01 13:46:57 +01:00 |
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sofstam
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38a818fd17
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Apply review suggestions
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2022-12-01 13:42:21 +01:00 |
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James A. Fellows Yates
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ef1d2da179
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-12-01 12:53:34 +01:00 |
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sofstam
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1965ade961
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Update schema
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2022-12-01 11:32:51 +01:00 |
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sofstam
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e5bb627402
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Apply review suggestions
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2022-12-01 11:12:31 +01:00 |
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James Fellows Yates
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bc98f5b80f
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Separate KrakenUniq test run
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2022-12-01 10:37:14 +01:00 |
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nf-core-bot
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8067012c01
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[automated] Fix linting with Prettier
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2022-12-01 09:15:35 +00:00 |
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James A. Fellows Yates
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4f6eb6fd75
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Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
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2022-12-01 09:03:29 +01:00 |
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sofstam
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933b820c19
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Apply review suggestions
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2022-11-29 16:57:07 +01:00 |
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Sofia Stamouli
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e85c75dcba
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Merge branch 'dev' into update_motus
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2022-11-29 15:12:31 +01:00 |
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sofstam
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12dd836e9c
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Fix conflict
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2022-11-29 15:00:27 +01:00 |
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sofstam
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f389029848
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Fix merge conflic
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2022-11-29 14:38:39 +01:00 |
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James Fellows Yates
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d7fbe55849
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Add KU to the test profiles and add id to KU processes
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2022-11-29 14:19:01 +01:00 |
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