James A. Fellows Yates
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8456f934ed
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Update subworkflows/local/visualization_krona.nf
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2022-09-02 16:15:46 +02:00 |
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James A. Fellows Yates
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13e9957e14
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Fixes process selector warning
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2022-09-02 06:03:05 +00:00 |
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James Fellows Yates
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d19a473c59
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Merge branch 'filtlong-in-tests' into json-schema
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2022-08-30 14:33:19 +02:00 |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2022-08-30 14:08:05 +02:00 |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2022-08-30 13:58:58 +02:00 |
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James Fellows Yates
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d4af88e3ff
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Make kaiju parameter clearer for documentation purpses and update documentation
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2022-08-25 15:50:28 +02:00 |
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James A. Fellows Yates
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de70b0a01d
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Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
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2022-07-29 13:36:25 +02:00 |
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James A. Fellows Yates
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f48b22d615
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Apply suggestions from code review
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2022-07-29 09:52:49 +02:00 |
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James Fellows Yates
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873a13e028
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Merge remote-tracking branch 'origin/dev' into porechop-log
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2022-07-29 09:51:34 +02:00 |
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Mahwash Jamy
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49487593e2
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Merge branch 'nf-core:dev' into diamond-update
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2022-07-28 15:48:59 +02:00 |
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sofstam
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cecbb41f88
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Update centrifuge/kreport
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2022-07-27 14:42:35 +02:00 |
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James A. Fellows Yates
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9d2be68fb8
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Merge branch 'dev' into centrifuge_mqc
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2022-07-26 18:01:30 +00:00 |
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James A. Fellows Yates
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1ef0975736
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Merge branch 'dev' into porechop-log
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2022-07-26 18:00:28 +00:00 |
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James A. Fellows Yates
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3054dea7c2
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Get multiqc input working
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2022-07-26 08:41:06 +00:00 |
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James A. Fellows Yates
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e76b299705
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Start working getting kraken and centrifuge working in MQC
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2022-07-26 08:18:54 +00:00 |
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James Fellows Yates
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139cf0d6aa
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Fix
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2022-07-26 10:12:33 +02:00 |
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James A. Fellows Yates
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64f01fcfe0
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Merge branch 'dev' into porechop-log
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2022-07-20 14:05:23 +02:00 |
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James Fellows Yates
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255afee4c7
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Re-add the collects
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2022-07-19 17:10:10 +02:00 |
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Mahwash Jamy
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811ded38af
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Update subworkflows/local/profiling.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-07-19 16:44:48 +02:00 |
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Sofia Stamouli
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237e9aa623
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Update longread_preprocessing.nf
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2022-07-19 16:44:08 +02:00 |
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James A. Fellows Yates
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8d7ddb5847
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Apply suggestions from code review
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2022-07-19 16:30:13 +02:00 |
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mjamy
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c4c82212e1
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incorporate diamond log file into multiqc channel
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2022-07-19 14:12:16 +02:00 |
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sofstam
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171258d545
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Fix typos
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2022-07-19 14:07:13 +02:00 |
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sofstam
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25bc01f9c4
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Fix typos
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2022-07-19 14:04:49 +02:00 |
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sofstam
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8147dba0b4
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Fix typos
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2022-07-19 14:03:10 +02:00 |
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sofstam
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526ed79763
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Fix filtlong logs
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2022-07-19 14:01:11 +02:00 |
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sofstam
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1ba6a08135
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Seperate multiqc for filtlong
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2022-07-19 13:53:29 +02:00 |
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James Fellows Yates
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33a5402b25
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Add emitting porechop logs to multiqc and fix collection of others
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2022-07-19 13:50:39 +02:00 |
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sofstam
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3f5fa8cc7a
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Merge branch 'dev' into update_filtlong
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2022-07-19 13:50:28 +02:00 |
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sofstam
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5a2fd260fd
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Log file into multiqc channel
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2022-07-15 12:50:50 +02:00 |
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James A. Fellows Yates
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c215ed5607
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Merge branch 'dev' into motus/merge
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2022-07-15 10:52:42 +02:00 |
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James A. Fellows Yates
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cc3967a3fd
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Apply suggestions from code review
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2022-07-15 10:51:41 +02:00 |
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James Fellows Yates
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31119f83c2
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Send to MQC only the log file not the meta
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2022-07-13 14:29:47 +02:00 |
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James Fellows Yates
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13280e2468
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Fix .empty
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2022-07-13 12:44:44 +02:00 |
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James Fellows Yates
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eaa69b65d8
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Update mOTUs profile module and mix log for multiqc
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2022-07-13 12:38:30 +02:00 |
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James Fellows Yates
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c22946cfab
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Fix motu versions not being exported if not run
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2022-07-13 12:36:29 +02:00 |
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James Fellows Yates
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a0ee82bf43
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Add motus/merge and biom support
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2022-07-12 11:39:26 +02:00 |
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James A. Fellows Yates
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8082c7d108
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Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
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2022-07-05 15:17:52 +02:00 |
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James A. Fellows Yates
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26e31c782d
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Merge branch 'dev' into motus
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2022-07-04 13:14:42 +02:00 |
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James Fellows Yates
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02c06b9f7b
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Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
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2022-06-30 18:33:11 +02:00 |
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James Fellows Yates
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27f174d17e
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Merge remote-tracking branch 'origin/dev' into malt-to-krona
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2022-06-30 12:01:33 +02:00 |
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James Fellows Yates
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0050f45345
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Add taxonomy directory param
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2022-06-30 11:43:52 +02:00 |
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6673ccf8d8
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Update channel assignment alignment in profiling subworkflow
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-06-28 09:00:43 -05:00 |
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4de43040a3
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Switch to using raw classifications for Kaiju2Krona
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2022-06-28 09:00:41 -05:00 |
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821dd844d8
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Add Kaiju profile conversion to visualization workflow
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2022-06-27 09:23:20 -05:00 |
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23fec89b06
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Add Krona chart creation for Centrifuge reports
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2022-06-27 08:52:29 -05:00 |
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a40a442178
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Create VISUALIZATION_KRONA workflow to create Krona charts
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2022-06-27 08:22:47 -05:00 |
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James Fellows Yates
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e0ad49ebc9
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Fix metadata manipulaton for malt
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2022-06-10 19:33:37 +02:00 |
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James A. Fellows Yates
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621b6a3d09
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Add comments about MALT id replacement and refactor for simplicity
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2022-06-10 11:27:51 +02:00 |
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James A. Fellows Yates
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ebdd5683b2
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Apply suggestions from code review
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2022-06-03 22:33:48 +02:00 |
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