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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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 A. Fellows Yates
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971f6a6ea8
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Merge pull request #190 from nf-core/motus-update-version
Update mOTUs to 3.0.3
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2022-12-12 18:24:05 +01:00 |
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sofstam
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4756dc7f0d
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Update output.md
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2022-12-12 17:14:57 +01:00 |
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sofstam
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b1eb477f33
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Update output.md
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2022-12-12 17:06:05 +01:00 |
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Sofia Stamouli
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a99f89af77
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Apply review suggestions
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2022-12-12 16:30:28 +01:00 |
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James Fellows Yates
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e31e7d3172
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Update mOTUs to 3.0.3
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2022-12-12 15:42:01 +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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Apply review suggestions
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2022-12-12 13:19:59 +01:00 |
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James A. Fellows Yates
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be85cb408c
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Merge pull request #188 from nf-core/bracken-mergetables
Add Bracken mergetables
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2022-12-12 11:26:19 +01:00 |
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James Fellows Yates
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7c66968fef
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More comments
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2022-12-12 11:04:21 +01:00 |
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James Fellows Yates
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460f3ca157
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Add database sheet validation
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2022-12-12 11:03:40 +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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sofstam
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c9a6320dac
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Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output
Conflicts:
docs/output.md
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2022-12-12 09:13:02 +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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sofstam
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b35d26744d
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Add classifiers
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2022-12-09 17:11:48 +01:00 |
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Sofia Stamouli
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6d0b5d0a58
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Prettier
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2022-12-09 15:38:59 +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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sofstam
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c5f4c9486a
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Start the documentation of output.md
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2022-12-09 15:30:11 +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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