nvnieuwk
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95e8afe627
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Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile
added gatk4/composestrtablefile
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2022-06-01 09:33:08 +02:00 |
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Nicolas Vannieuwkerke
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114a54c8d5
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spaces fix
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2022-06-01 09:22:09 +02:00 |
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Nicolas Vannieuwkerke
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8470f3cb7e
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linting
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2022-06-01 09:20:20 +02:00 |
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James A. Fellows Yates
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5a94794793
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Merge branch 'master' into r-ampir
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2022-06-01 09:18:54 +02:00 |
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Nicolas Vannieuwkerke
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d4f3df4677
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Updated the test
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2022-06-01 09:17:05 +02:00 |
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nvnieuwk
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5b74a179c3
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Update modules/gatk4/composestrtablefile/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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2022-06-01 09:14:08 +02:00 |
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nvnieuwk
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e4f51d6f59
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Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile
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2022-06-01 08:59:19 +02:00 |
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Alexander Peltzer
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9ac3cf342a
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Merge branch 'master' into gatk-realigntargetcreator
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2022-05-31 21:12:59 +02:00 |
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James A. Fellows Yates
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33af85697b
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Merge pull request #1713 from jfy133/fix-filtlong
Fix filtlong to remove hardcoded output names
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2022-05-31 20:50:21 +02:00 |
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James Fellows Yates
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7633d7816b
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Add GATK(3)/realignertargetcreator
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2022-05-31 20:35:54 +02:00 |
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James A. Fellows Yates
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615cb0722f
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Merge branch 'master' into fix-filtlong
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2022-05-31 20:25:16 +02:00 |
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James Fellows Yates
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d39ba08e02
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Prepare main module code
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2022-05-31 20:19:49 +02:00 |
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James Fellows Yates
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c1ac3fbb59
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Skeleton
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2022-05-31 20:13:48 +02:00 |
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James Fellows Yates
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df22cd80df
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Fix config for tests
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2022-05-31 20:07:52 +02:00 |
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FriederikeHanssen
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fba7edb652
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Merge pull request #1716 from asp8200/get_tbi_files_from_gatk4_mergevcfs
Get tbi-files from gatk4 mergevcfs
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2022-05-31 17:55:06 +02:00 |
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FriederikeHanssen
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19037ed8f4
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Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs
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2022-05-31 17:42:27 +02:00 |
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asp8200
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4199a05aeb
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Removing redundant empty line
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2022-05-31 15:34:34 +00:00 |
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Nicolas Vannieuwkerke
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1166fb5150
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prettier
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2022-05-31 16:13:38 +02:00 |
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Nicolas Vannieuwkerke
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ec41ea6082
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fix test.yml
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2022-05-31 16:12:05 +02:00 |
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Nicolas Vannieuwkerke
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80366924fd
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added gatk4/composestrtablefile
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2022-05-31 16:08:13 +02:00 |
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asp8200
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98bb45cf4e
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Updating test for gatk4/mergevcfs
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2022-05-31 13:59:56 +00:00 |
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SusiJo
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84f584875e
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change string array
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2022-05-31 15:50:31 +02:00 |
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James Fellows Yates
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089f761f0b
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Actually add the changes
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2022-05-31 15:49:57 +02:00 |
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James A. Fellows Yates
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edc9e83a7d
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Merge branch 'master' into fix-filtlong
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2022-05-31 15:47:39 +02:00 |
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James Fellows Yates
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3e20ca7e9a
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Don't hardcode forced output names
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2022-05-31 15:46:28 +02:00 |
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SusiJo
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58389e550d
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test json array
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2022-05-31 15:41:50 +02:00 |
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Anders Sune Pedersen
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5513d095f5
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Adding tbi-files to the output from GATK4_MERGEVCFS. #1709
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2022-05-31 15:37:26 +02:00 |
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SusiJo
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49135415ae
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Merge branch 'master' into gatk_spark
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2022-05-31 15:36:55 +02:00 |
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SusiJo
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941760f75d
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ran prettier
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2022-05-31 15:36:02 +02:00 |
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SusiJo
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35e296cd7d
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added brackets
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2022-05-31 15:35:34 +02:00 |
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nvnieuwk
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22a90dbd0f
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Merge pull request #1711 from nvnieuwk/add-tbi-to-bcftools-concat
Added optional input of index files to bcftools/concat
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2022-05-31 15:33:10 +02:00 |
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SusiJo
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37b543e3e7
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changed to tab
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2022-05-31 15:29:27 +02:00 |
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SusiJo
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810564deca
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Merge branch 'master' into gatk_spark
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2022-05-31 15:24:58 +02:00 |
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nvnieuwk
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a6c7635b73
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Merge branch 'master' into add-tbi-to-bcftools-concat
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2022-05-31 15:20:03 +02:00 |
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Nicolas Vannieuwkerke
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51b0a6e4f3
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Added optional input of index files to bcftools/concat
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2022-05-31 15:15:58 +02:00 |
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James A. Fellows Yates
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94dd8f63df
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Merge pull request #1710 from jfy133/fix-filtlong
Fix filtlong - makes running without shortreads work correctly, and also ensures all tests produce …
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2022-05-31 14:54:54 +02:00 |
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SusiJo
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9ef09e6add
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adjusted newlines
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2022-05-31 14:54:39 +02:00 |
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SusiJo
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205576279f
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ran prettier again
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2022-05-31 14:50:55 +02:00 |
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James A. Fellows Yates
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0b895871d7
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Merge branch 'master' into fix-filtlong
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2022-05-31 14:49:44 +02:00 |
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James Fellows Yates
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430def06fa
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Switch from md5sum to string due to conda flakiness
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2022-05-31 14:45:41 +02:00 |
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SusiJo
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d484aa1906
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adjusted tabs
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2022-05-31 14:45:23 +02:00 |
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SusiJo
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e083bfafa0
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ran prettier
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2022-05-31 14:38:45 +02:00 |
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SusiJo
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1e396d767f
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Merge remote-tracking branch 'upstream/master' into gatk_spark
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2022-05-31 14:36:14 +02:00 |
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SusiJo
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ea526051a4
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new test.yml
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2022-05-31 14:35:42 +02:00 |
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SusiJo
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3117b2973c
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added test for metrics
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2022-05-31 14:35:29 +02:00 |
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SusiJo
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e0e8273f74
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adjusted input to use queryname sorted bams
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2022-05-31 14:35:18 +02:00 |
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SusiJo
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39e34418c9
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added metrics as optional output
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2022-05-31 14:34:50 +02:00 |
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James A. Fellows Yates
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667a0bc24c
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Merge pull request #1708 from sguizard/bamtools/convert/remove_TODO
👌 IMPROVE: Remove last TODO
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2022-05-31 13:41:41 +02:00 |
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James Fellows Yates
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723852bf3d
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Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files
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2022-05-31 13:38:18 +02:00 |
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James Fellows Yates
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7ffe98ac8b
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Add gatk/indelrealigner
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2022-05-30 21:12:21 +02:00 |
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