James A. Fellows Yates
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8dd711aba2
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Update tests/modules/motus/profile/main.nf
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2022-05-12 20:08:37 +01:00 |
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FriederikeHanssen
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868150e1af
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Merge branch 'master' into gatk_426
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2022-05-12 19:33:07 +02:00 |
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Rike
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99880654bf
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add output default bam
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2022-05-12 18:06:15 +02:00 |
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Rike
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8792d102ee
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fix test input
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2022-05-12 17:37:06 +02:00 |
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Rike
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a694267b4b
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fix empty index input
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2022-05-12 17:01:03 +02:00 |
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Rike
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b3bd55da76
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getpileupsummaries requires intervals files
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2022-05-12 16:51:17 +02:00 |
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Rike
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15fbf21b28
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double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere
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2022-05-12 16:16:53 +02:00 |
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Rike
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fef5434c4c
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Update md5sums
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2022-05-12 16:07:12 +02:00 |
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Jasmin F
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85b3c2bcf2
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-12 15:28:19 +02:00 |
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James A. Fellows Yates
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3c02e6056c
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Merge branch 'master' into antismashlite
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2022-05-12 14:53:52 +02:00 |
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jasmezz
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d2ef476321
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Fix Prettier linting error
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2022-05-12 12:19:50 +02:00 |
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jasmezz
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37cc6f250b
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Fixed test.yml
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2022-05-12 12:14:19 +02:00 |
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Chris Cheshire
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90c67794bf
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Added extra tests but error with collection
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2022-05-12 10:01:33 +01:00 |
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jasmezz
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bd4b70439b
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Streamlined some output channels, formatted tests main.nf
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2022-05-12 10:56:48 +02:00 |
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Matthias De Smet
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dcf9c07fc9
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Merge branch 'master' into update/bowtie2-align
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2022-05-11 19:08:23 +02:00 |
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Moritz E. Beber
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98d8a741ec
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tests: add missing paths to config
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2022-05-11 18:17:27 +02:00 |
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Moritz E. Beber
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888620063b
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tests: delete settings for conda
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2022-05-11 17:44:49 +02:00 |
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Moritz E. Beber
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b2dbaa9930
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refactor: rename module
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2022-05-11 17:33:45 +02:00 |
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Moritz E. Beber
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23091aabda
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refactor: move files to custom section
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2022-05-11 17:33:45 +02:00 |
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Moritz E. Beber
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a83dd33a7e
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tests: use remove settings file
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2022-05-11 17:33:45 +02:00 |
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Moritz E. Beber
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e4551a9ab3
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refactor: always output settings
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2022-05-11 17:33:45 +02:00 |
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Moritz E. Beber
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64ff23f3c1
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feat: add module that verifies NCBI settings
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2022-05-11 17:33:45 +02:00 |
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Jasmin F
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853e3ec087
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Remove commented code
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-05-11 15:56:10 +02:00 |
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Matthias De Smet
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94e8c3a882
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Update tests/modules/bowtie2/align/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2022-05-11 13:56:03 +02:00 |
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Matthias De Smet
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0d00452eca
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Update tests/modules/bowtie2/align/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2022-05-11 13:55:45 +02:00 |
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Matthias De Smet
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dcffd93875
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Merge branch 'master' into update/bowtie2-align
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2022-05-11 13:34:24 +02:00 |
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CMGG ICT Team
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3ae8cbfad7
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bowtie2: remove code duplication
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2022-05-11 13:32:56 +02:00 |
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Moritz E. Beber
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0cdf7767a7
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refactor: require NCBI user settings always
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2022-05-11 13:02:52 +02:00 |
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Moritz E. Beber
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eae7161a32
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tests: add settings input or not and test all branches
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2022-05-11 12:47:54 +02:00 |
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Mahesh Binzer-Panchal
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00fcdd0cba
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Merge branch 'master' into genomescope2
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2022-05-11 12:42:39 +02:00 |
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Mahesh Binzer-Panchal
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d54cf467f4
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Update outputs and test data set
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2022-05-11 10:42:17 +00:00 |
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Harshil Patel
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7be7f404d5
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Merge branch 'master' into refactor-prefetch
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2022-05-11 11:28:02 +01:00 |
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jasmezz
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2b746abfbe
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Fix Prettier linting issue
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2022-05-11 12:09:52 +02:00 |
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jasmezz
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5d76f1c7ff
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Add fasta/gff input option
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2022-05-11 12:06:02 +02:00 |
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Jasmin F
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9cce4a00b2
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Merge branch 'nf-core:master' into antismashlite
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2022-05-11 12:03:30 +02:00 |
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Mahesh Binzer-Panchal
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0774704038
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Merge branch 'master' into genomescope2
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2022-05-11 11:38:36 +02:00 |
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Praveen Raj S
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237971cd15
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Merge branch 'master' into master
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2022-05-10 14:35:41 +02:00 |
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Nicolas Vannieuwkerke
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b7134855e4
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Small update on the output channels
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2022-05-10 12:34:52 +02:00 |
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Moritz E. Beber
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1b228835e9
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refactor: require settings input always
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2022-05-10 12:29:42 +02:00 |
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Moritz E. Beber
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145e2f80e9
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tests: run prefetch with and without given settings
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2022-05-10 12:16:57 +02:00 |
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Nicolas Vannieuwkerke
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3a064b0a99
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Split the output to different channels
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2022-05-10 12:05:42 +02:00 |
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Nicolas Vannieuwkerke
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6008619603
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test issue fix?
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2022-05-10 10:20:54 +02:00 |
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Nicolas Vannieuwkerke
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96c3f895b9
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test issue fix?
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2022-05-10 10:19:13 +02:00 |
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Nicolas Vannieuwkerke
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42fbf80c72
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Fixed a test issue with wrong md5sum
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2022-05-10 09:57:49 +02:00 |
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Nicolas Vannieuwkerke
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f0e8f6ce4d
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Linting
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2022-05-10 09:36:54 +02:00 |
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Nicolas Vannieuwkerke
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e5d091ad4b
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Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval
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2022-05-10 09:35:44 +02:00 |
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Nicolas Vannieuwkerke
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c69d5cc23e
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Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)
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2022-05-10 09:35:42 +02:00 |
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nvnieuwk
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95103fbd79
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-10 09:06:34 +02:00 |
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Praveen Raj S
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459a2d1759
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Merge branch 'master' into master
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2022-05-09 22:16:59 +02:00 |
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Mahesh Binzer-Panchal
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f65d896f57
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create genomescope2 module
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2022-05-09 15:09:15 +00:00 |
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Mahesh Binzer-Panchal
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705ad7c3a1
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Merge branch 'master' into meryl_unionsum
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2022-05-09 16:20:01 +02:00 |
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nvnieuwk
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aceb5220cf
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-09 16:18:00 +02:00 |
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Mahesh Binzer-Panchal
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83a266ea70
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Merge branch 'master' into meryl_unionsum
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2022-05-09 16:16:08 +02:00 |
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FriederikeHanssen
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adc4ff868c
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Merge branch 'master' into samtools_convert
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2022-05-09 16:15:24 +02:00 |
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nvnieuwk
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4b8bd9ebf9
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-09 15:51:31 +02:00 |
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Mahesh Binzer-Panchal
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da93beaf60
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Update pytests
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2022-05-09 13:50:49 +00:00 |
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Nicolas Vannieuwkerke
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f6262b4a10
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fixed some issues
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2022-05-09 15:47:07 +02:00 |
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Mahesh Binzer-Panchal
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8d86988632
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Merge branch 'master' into meryl/histogram
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2022-05-09 15:39:32 +02:00 |
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nvnieuwk
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d6dd4c2e2d
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Update tests/modules/rtgtools/vcfeval/test.yml
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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2022-05-09 15:35:16 +02:00 |
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Rike
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ef5f145342
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Generalize Bam2Cram do either conversion
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2022-05-09 15:22:54 +02:00 |
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Annick Renevey
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ac3034696b
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update md5sum
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2022-05-09 15:19:16 +02:00 |
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Mahesh Binzer-Panchal
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f0f414d519
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Update pytests
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2022-05-09 13:00:10 +00:00 |
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Annick Renevey
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eed874ace7
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update arriba tests
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2022-05-09 14:55:59 +02:00 |
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Mahesh Binzer-Panchal
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6621768550
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Update pytest outputs
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2022-05-09 12:54:31 +00:00 |
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Mahesh Binzer-Panchal
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ce97c87b5d
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Merge branch 'master' into meryl_unionsum
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2022-05-09 13:51:55 +02:00 |
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Mahesh Binzer-Panchal
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a43bc940d6
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Add suggestions from code review
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2022-05-09 11:15:14 +00:00 |
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Mahesh Binzer-Panchal
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129f57ccd9
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Add meryl histogram
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2022-05-09 08:50:28 +00:00 |
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Mahesh Binzer-Panchal
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ad4f8389cb
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Add meryl unionsum
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2022-05-09 08:33:21 +00:00 |
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Mahesh Binzer-Panchal
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32b0fdc9d9
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Merge branch 'master' into meryl_count
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2022-05-09 10:05:28 +02:00 |
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Mahesh Binzer-Panchal
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9ebeb6a702
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Update test
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2022-05-09 08:05:07 +00:00 |
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Matthias De Smet
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3dc18365f6
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-09 10:04:29 +02:00 |
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Mahesh Binzer-Panchal
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4591ea2205
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atomize
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2022-05-09 07:58:58 +00:00 |
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Matthias De Smet
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2b91985aa0
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-09 09:43:48 +02:00 |
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Nicolas Vannieuwkerke
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d18af7358a
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Moved untarring the genome sdf folder to the test itself
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2022-05-09 09:20:42 +02:00 |
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Lucpen
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bdaed264a7
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Merge branch 'master' into correcting_stubs
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2022-05-09 08:54:22 +02:00 |
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James A. Fellows Yates
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8a83ad0518
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Merge branch 'master' into motus_profile
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2022-05-09 08:16:16 +02:00 |
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Matthias De Smet
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0752b82c9f
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Merge branch 'master' into update/snapaligner
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2022-05-06 18:57:37 +02:00 |
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Matthias De Smet
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dd458e3388
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fix tags
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2022-05-06 18:57:17 +02:00 |
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Mahesh Binzer-Panchal
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67481c6d54
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Start Meryl count
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2022-05-06 15:04:04 +00:00 |
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nvnieuwk
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5153e10840
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Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-06 16:19:17 +02:00 |
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Lucpen
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8e5fda3b10
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Merge branch 'master' into correcting_stubs
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2022-05-06 15:37:08 +02:00 |
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Lucpen
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971a17a3ab
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fix datatest for stubs
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2022-05-06 15:34:18 +02:00 |
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Mahesh Binzer-Panchal
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7a85760d08
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remove 'auto' test
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2022-05-06 13:33:27 +00:00 |
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Lucpen
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0fa36e6777
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fix added correct entry workflow in test.yml
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2022-05-06 15:26:34 +02:00 |
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JIANHONG OU
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9b50036e9b
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add test_bam and -m parameter for motus_profile
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2022-05-06 08:56:42 -04:00 |
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JIANHONG OU
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c301a406dd
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Merge branch 'nf-core:master' into motus_profile
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2022-05-06 08:33:43 -04:00 |
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Nicolas Vannieuwkerke
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84b354ab6a
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Added the rtgtools/vcfeval module
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2022-05-06 14:23:40 +02:00 |
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JIANHONG OU
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26d5b4da72
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Update tests/modules/motus/profile/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 08:19:54 -04:00 |
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Matthias De Smet
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3930ba227b
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merge snapaligner modes into one
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2022-05-06 14:10:44 +02:00 |
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Mahesh Binzer-Panchal
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a9f23bb477
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Merge branch 'master' into busco
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2022-05-06 13:49:01 +02:00 |
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Mahesh Binzer-Panchal
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35c5828f43
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Add --auto-lineage option and remove single_end
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
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2022-05-06 11:48:21 +00:00 |
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Jose Espinosa-Carrasco
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035655e35d
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Merge branch 'master' into modules/md5sum
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2022-05-06 12:34:14 +02:00 |
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Matthias De Smet
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09e729ad41
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added sha256sum
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2022-05-06 10:28:14 +02:00 |
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Matthias De Smet
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853b623969
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new module: md5sum
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2022-05-06 09:20:40 +02:00 |
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Ramprasad Neethiraj
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db56d80060
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Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor
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2022-05-06 00:10:28 +02:00 |
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Ramprasad Neethiraj
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e4e4f8090c
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combine multiple pytor
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2022-05-05 23:59:12 +02:00 |
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JIANHONG OU
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b8efa2ae7c
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Merge branch 'master' into motus_profile
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2022-05-05 13:41:54 -04:00 |
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JIANHONG OU
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fb5c5d310a
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update motus module.
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2022-05-05 13:38:46 -04:00 |
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Sateesh Peri
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faf45edc5e
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Merge branch 'master' into busco
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2022-05-05 12:48:39 -04:00 |
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Ramprasad Neethiraj
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db2acba71b
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Merge branch 'master' into feat/update_cnvpytor
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2022-05-05 17:31:10 +02:00 |
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