James A. Fellows Yates
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45ac6fedc2
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Merge pull request #237 from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
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2023-02-09 10:59:27 +01:00 |
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James A. Fellows Yates
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70eb84b8d5
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2023-02-09 08:01:52 +01:00 |
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James Fellows Yates
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18886c0cbc
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Start trying a different method with maps in profiling
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2023-02-07 15:51:25 +01:00 |
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James Fellows Yates
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059cd17114
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Fix exporting of mapped/unmapped reads for consistency across both short and long reads
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2023-02-07 11:43:40 +01:00 |
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sofstam
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5363274867
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Add some last documentation
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2023-02-02 13:58:48 +01:00 |
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James Fellows Yates
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7ce55a99e8
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Fix linting
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2023-02-02 13:08:16 +01:00 |
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James A. Fellows Yates
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c4e366d47d
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Add full test data and documentation of the test data
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2023-02-02 11:59:26 +01:00 |
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James A. Fellows Yates
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1d7da61801
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
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2023-01-30 11:25:28 +01:00 |
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James A. Fellows Yates
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098ec087c9
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Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
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2023-01-25 13:48:06 +01:00 |
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James Fellows Yates
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a993300099
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Tweaks to MultiQC based on full test experiments
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2023-01-24 15:06:42 +01:00 |
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James Fellows Yates
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e7d7affcd0
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Pick up Kraken2 files correctly
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2023-01-24 14:44:14 +01:00 |
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Moritz E. Beber
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40f1e7b27a
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fix: correct pattern to publish minimap2 index
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2023-01-24 14:15:51 +01:00 |
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James Fellows Yates
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1c820f21b3
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Dont fail on divide by 0 errors on centrifuge
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2023-01-20 17:53:55 +01:00 |
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James A. Fellows Yates
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d9003924be
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Merge pull request #201 from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
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2023-01-19 13:15:14 +01:00 |
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James Fellows Yates
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92dff9b453
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Standardise file names using only underscore
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2023-01-17 10:58:30 +01:00 |
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James Fellows Yates
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c8f6d713a3
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Add tool names to end of prefix files for easier distinguishing in general stats
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2023-01-16 14:49:44 +01:00 |
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James Fellows Yates
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d6fa45b500
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update MultiQC and include latest modules
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2023-01-16 14:39:52 +01:00 |
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James A. Fellows Yates
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25bb4304e8
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Merge pull request #187 from nf-core/revert-pep
Revert PEP validation back to python samplesheet check
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2022-12-20 15:03:18 +01:00 |
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Sofia Stamouli
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c23eb968f9
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Remove TODOs from test configs
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2022-12-16 15:20:06 +01:00 |
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James Fellows Yates
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9e6a91aff9
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Distinguish Kraken2 from Bracken
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2022-12-15 13:25:01 +01:00 |
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James Fellows Yates
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3b86a22556
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Fix falco publication names
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2022-12-15 12:57:49 +01:00 |
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James Fellows Yates
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88589fbc53
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Fix publishing of log files of rpreprocessing steps
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2022-12-15 10:35:06 +01:00 |
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James A. Fellows Yates
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578081df2e
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Merge pull request #189 from nf-core/database-check
Adds (native groovy!) database check
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2022-12-13 08:43:00 +01:00 |
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James Fellows Yates
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3df0a383da
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Update combine bracken outputs to include meta for publishing purposes
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2022-12-12 10:10:24 +01:00 |
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James Fellows Yates
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07bd989bc6
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Start work on groovy native datbase checks
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2022-12-12 10:02:22 +01:00 |
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James Fellows Yates
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4b68e95770
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Revert PEP validation back to python samplesheet check
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2022-12-12 08:49:13 +01:00 |
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James Fellows Yates
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8939ce3e20
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Start adding bracken/combinebrackenreports (need smodule update)
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2022-12-11 16:52:34 +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 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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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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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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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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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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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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Sofia Stamouli
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7e3ece53bd
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Update modules.config
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2022-11-29 13:31:00 +01:00 |
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Sofia Stamouli
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0088b07220
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Fix trailing whitespace
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2022-11-29 13:28:04 +01:00 |
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James A. Fellows Yates
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770a35d7ac
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Update conf/modules.config
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2022-11-29 12:49:20 +01:00 |
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Sofia Stamouli
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ba727a81ae
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Fix left-padding spaces
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2022-11-29 12:45:14 +01:00 |
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Sofia Stamouli
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71b52b9c94
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Apply review suggestions
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2022-11-29 11:58:23 +01:00 |
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sofstam
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49af33f68e
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Include NCBI_id, read counts and mgc arguments in motus
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2022-11-29 11:07:29 +01:00 |
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James A. Fellows Yates
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f114cc4122
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Apply suggestions from code review
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2022-11-24 16:55:19 +01:00 |
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James A. Fellows Yates
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17b1e3df1c
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Update test.config
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2022-11-24 16:53:39 +01:00 |
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James Fellows Yates
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a20b3e3c58
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Try to reduce MALT memory
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2022-11-24 15:51:12 +01:00 |
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