Mahwash Jamy
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3147a80a56
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Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module
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2022-10-31 15:36:57 +00:00 |
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Sofia Stamouli
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1bd6dbfe58
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Add samtools stats for long-reads
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2022-10-28 11:40:50 +02:00 |
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Moritz E. Beber
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bf89525bc2
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Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
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2022-10-27 17:35:06 +02:00 |
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Mahwash Jamy
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36e101a78b
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Install krakenuniq module
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2022-10-25 09:26:33 +00:00 |
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Sofia Stamouli
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8eddb32b88
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Add Falco as an alternative to FastQC
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2022-10-18 17:43:16 +02:00 |
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Moritz E. Beber
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563b34c9c3
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refactor: rename process to kraken2
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2022-10-14 14:48:27 +02:00 |
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Moritz E. Beber
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7f8180f458
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fix: emit tool versions
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2022-10-14 12:49:07 +02:00 |
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Moritz E. Beber
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ca38d002de
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feat: integrate Bracken into the profiling pipeline
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2022-10-14 12:18:07 +02:00 |
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Moritz E. Beber
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4f728648f5
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feat: add process to standardize kraken report
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2022-10-14 10:56:14 +02:00 |
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Moritz E. Beber
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4352d35937
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chore: install Bracken module
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2022-10-14 10:52:17 +02:00 |
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James Fellows Yates
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56bae85755
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Remove necessity of patch
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2022-10-11 12:38:18 +02:00 |
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Moritz E. Beber
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5f3dbd28de
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fix: patch inputs to correspond to previous version
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2022-10-05 13:51:15 +02:00 |
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Moritz E. Beber
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b407fbcdce
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chore: force update all modules
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2022-10-05 12:24:18 +02:00 |
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Moritz E. Beber
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fdb8a7f740
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Merge branch 'devel' into nf-core-template-merge-2.6
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2022-10-05 12:21:54 +02:00 |
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nf-core-bot
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51bacb00e6
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Template update for nf-core/tools version 2.6
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2022-10-05 03:30:53 +00:00 |
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James A. Fellows Yates
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3ca9058b9c
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Merge pull request #133 from rafalstepien/add-pep-support
Add working version of PEP-nf-core integration
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2022-09-30 10:21:15 +02:00 |
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James Fellows Yates
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43a8aa4405
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Remove detect_reads.py and replace remaining checks with nextflow code instead
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2022-09-27 15:32:51 +02:00 |
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Rafal Stepien
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e84b64f7e1
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Update modules/local/samplesheet_check.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-09-19 09:49:20 -04:00 |
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Rafal Stepien
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9349346864
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Remove --pep parameter and leave just --input
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2022-09-16 10:14:01 -04:00 |
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James A. Fellows Yates
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016efcb807
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-16 16:02:38 +02:00 |
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James Fellows Yates
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c5cc21d29e
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Update motus merge module to remove unused channel
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2022-09-16 10:25:24 +02:00 |
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James Fellows Yates
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4e7857e2ed
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Standardise mOTUs table merge
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2022-09-16 08:36:34 +02:00 |
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James A. Fellows Yates
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cdb21d17b3
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Merge branch 'dev' into metaphlan3/mergemetaphlantables
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2022-09-15 13:08:57 +02:00 |
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James Fellows Yates
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21ae9d85c3
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Ensure merge metaphlan3 tables happens on per database basis
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2022-09-15 12:29:54 +02:00 |
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Rafal Stepien
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5f3eee9a4a
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Add working version of PEP-nf-core integration
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2022-09-14 14:28:48 -04:00 |
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James Fellows Yates
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abbbf9c7ab
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Update to use tar module compatible for our test databases
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2022-09-14 11:16:28 +02:00 |
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James Fellows Yates
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c8dbf5be47
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Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
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2022-09-13 15:47:28 +02:00 |
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James Fellows Yates
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a764bc4807
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Start works - need updated module though t have meta
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2022-09-09 13:57:06 +02:00 |
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James Fellows Yates
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f087136ec9
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use proper working FASTP module
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2022-09-09 11:12:47 +02:00 |
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James Fellows Yates
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60224e9149
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Patch fastp until I have an OK on the module update
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2022-09-08 14:25:23 +02:00 |
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James Fellows Yates
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fc26948950
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Fix MultiQC
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2022-09-08 12:49:38 +02:00 |
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James Fellows Yates
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d11257b330
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Module update
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2022-09-08 08:08:36 +02:00 |
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James A. Fellows Yates
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28d8d3f8fb
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Merge branch 'dev' into nf-core-template-merge-2.5
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2022-08-31 09:16:34 +02:00 |
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nf-core-bot
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6dfca81761
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Template update for nf-core/tools version 2.5
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2022-08-30 13:43:03 +00:00 |
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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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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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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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mjamy
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035b4b7a17
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Update the dev branch with the DIAMOND module update
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2022-07-15 16:28:07 +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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sofstam
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6b00360ff5
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Merge branch 'dev' into update_filtlong
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2022-07-15 10:05:43 +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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sofstam
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4a316df209
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Update the dev branch with the filtlong update
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2022-07-12 17:15:36 +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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447b8f0905
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Get fixed Krona module and add Krona taxonomy to test profile
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2022-07-01 17:21:19 +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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