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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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 A. Fellows Yates
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d7ca3df160
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Merge pull request #104 from nf-core/motus-profile-update
Update mOTUs profile module and mix log for multiqc
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2022-07-14 16:03:01 +02:00 |
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James Fellows Yates
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449b6a5553
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Fix file name output clashing wiht multiqc
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2022-07-13 15:25:58 +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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sofstam
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1fbe241d27
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Update filtlong module
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2022-07-12 17:43:52 +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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d8c0e9e7fe
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Prettier
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2022-07-12 11:41:07 +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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1eba859bf8
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Merge pull request #82 from jianhong/motus
add motus profile.
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2022-07-04 14:16:12 +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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97e6cdf4b4
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Add Krona taxonomy DB to schema build
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2022-06-30 18:36:13 +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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James A. Fellows Yates
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913080a5b1
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Merge pull request #96 from MillironX/feature/kaiju2krona
Add Krona output for Kaiju profiles
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2022-06-29 09:27:25 +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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069370db86
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Add unclassified and verbose flags to kaiju2krona
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2022-06-28 09:00:42 -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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James Fellows Yates
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af854f5f34
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Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files
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2022-06-28 12:42:41 +02:00 |
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James A. Fellows Yates
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e66c2b9b87
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Merge pull request #94 from MillironX/feature/centrifuge2krona
Add Krona output for Centrifuge profiles
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2022-06-27 17:13:31 +02:00 |
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James A. Fellows Yates
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5e554a3a0b
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Merge pull request #91 from MillironX/feature/kreport2krona
Add Krona output for Kraken classification
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2022-06-27 16:55:55 +02:00 |
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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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5b80c7cab9
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Install KAIJU_KAIJU2KRONA
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2022-06-27 08:58:28 -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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18284e6e32
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Add run_krona option to allow skipping Krona chart creation
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2022-06-27 08:45:08 -05:00 |
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15ac8b39fa
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Add citation for Krona
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2022-06-27 08:25:48 -05:00 |
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0e8edd5b2f
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Add output configuration for Kraken Krona chart
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2022-06-27 08:25:47 -05:00 |
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ad9bc4b7e9
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Add the visualization workflow to the main workflow
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2022-06-27 08:25:38 -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 A. Fellows Yates
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a83f53f64c
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Merge pull request #93 from nf-core/malt-rollback
MALT version rollback
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2022-06-20 09:43:09 +02:00 |
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James Fellows Yates
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4552b53e75
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Add note about MALT version to docs
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2022-06-20 08:30:23 +02:00 |
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James Fellows Yates
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4ff2145e44
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Roll back MALT version
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2022-06-20 08:23:14 +02:00 |
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James A. Fellows Yates
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2e7f26f380
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Replace header tuple with sub-set list of only relevant columns for sample checking
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2022-06-14 20:09:48 +00:00 |
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5da8d5b741
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Install KRONA_KTIMPORTTEXT
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2022-06-14 10:34:34 -05:00 |
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87678c127b
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Add KRONA_CLEANUP process module
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2022-06-14 10:34:33 -05:00 |
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a84f693479
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Install KRAKENTOOLS_KREPORT2KRONA module
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2022-06-14 08:13:36 -05:00 |
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James Fellows Yates
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c1a7d6335f
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Do not require fixed column order
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2022-06-13 21:02:12 +02:00 |
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James A. Fellows Yates
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3dcda7446b
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Merge pull request #86 from nf-core/support-aligned-reads
Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND
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2022-06-13 11:23:34 +02:00 |
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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 Fellows Yates
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6c6f5e0913
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Merge branch 'dev' of github.com:nf-core/taxprofiler into dev
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2022-06-09 08:21:51 +02:00 |
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James Fellows Yates
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ec13b8d608
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Remove support for uncompressed FASTQ files
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2022-06-09 08:21:48 +02:00 |
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James Fellows Yates
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800c0dd2aa
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Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads
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2022-06-09 08:16:01 +02:00 |
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