James Fellows Yates
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a565d9072a
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Add GATK UnifiedGenotyper
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2022-06-02 21:39:39 +02:00 |
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James Fellows Yates
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544b62df45
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Star work on GATK UG
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2022-06-02 21:11:17 +02:00 |
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James Fellows Yates
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9a4f22e8d1
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Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator
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2022-06-02 20:32:03 +02:00 |
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James Fellows Yates
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c469a2b35e
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Fux tests
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2022-06-02 20:32:00 +02:00 |
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James A. Fellows Yates
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abc619a3e2
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Merge branch 'master' into gatk-realigntargetcreator
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2022-06-02 20:24:24 +02:00 |
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SusiJo
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1b93cde9ff
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Merge branch 'master' into gatk_spark
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2022-06-02 16:24:39 +02:00 |
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Nicolas Vannieuwkerke
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b4b1f3b81d
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add intervals to calibratedragstrmodel
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2022-06-02 16:20:12 +02:00 |
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nvnieuwk
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e107d61069
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Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 14:20:15 +02:00 |
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nvnieuwk
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e419d306df
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Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 14:20:10 +02:00 |
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nvnieuwk
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2ce1cf3329
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Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 14:20:04 +02:00 |
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nvnieuwk
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a6c4276ad7
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Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 14:19:57 +02:00 |
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Nicolas Vannieuwkerke
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e53d091a6d
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added dragstr model to haplotypecaller
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2022-06-02 14:08:09 +02:00 |
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nvnieuwk
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a339f9818a
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Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
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2022-06-02 13:42:56 +02:00 |
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nvnieuwk
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4b430e8ece
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Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
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2022-06-02 13:41:20 +02:00 |
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Matthias De Smet
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f58771c47f
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Merge branch 'master' into update/untar
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2022-06-02 13:38:53 +02:00 |
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nvnieuwk
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eadab8e002
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Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
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2022-06-02 13:18:36 +02:00 |
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Nicolas Vannieuwkerke
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2a45d42868
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added the calibratedragstrmodel module
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2022-06-02 13:17:06 +02:00 |
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SusiJo
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2f3ddc90fb
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added fasta_fai as input + changed if statements
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2022-06-02 12:57:50 +02:00 |
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Matthias De Smet
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51be617b1c
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fix untar output dir
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2022-06-02 11:09:55 +02:00 |
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SusiJo
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7742661784
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Merge remote-tracking branch 'upstream/master' into cnvkit_bam
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2022-06-02 10:51:43 +02:00 |
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SusiJo
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a21cfb666e
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changed container + add cram2bam conversion
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2022-06-02 10:38:05 +02:00 |
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SusiJo
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9fc9be3e7b
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Merge remote-tracking branch 'origin/master' into cnvkit_bam
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2022-06-01 17:35:47 +02:00 |
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SusiJo
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f6953b5147
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adjust cnvkit/batch for germline mode
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2022-06-01 17:35:02 +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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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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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 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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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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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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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 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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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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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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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 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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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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jtangrot
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6ae405c5da
|
prettier
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2022-05-30 13:35:12 +02:00 |
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jtangrot
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6aac5c2c40
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Update test
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2022-05-30 13:30:27 +02:00 |
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jtangrot
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c67c15f243
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Make input tuple
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2022-05-30 13:01:06 +02:00 |
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jtangrot
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01d86439f5
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Add idcutoff as input
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2022-05-30 08:50:27 +02:00 |
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jtangrot
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589ce2d73a
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Add options for output file type
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2022-05-30 08:50:27 +02:00 |
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jtangrot
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1c99ffd876
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Add vserach usearch_global
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2022-05-30 08:50:27 +02:00 |
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Harshil Patel
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ad578cafcc
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Fix tests
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2022-05-27 12:14:10 +01:00 |
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Sateesh Peri
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ead3679829
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Merge branch 'master' into rp3-add-snippy
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2022-05-26 03:04:19 -04:00 |
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Harshil Patel
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241a1de035
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Update main.nf
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2022-05-25 19:38:12 +01:00 |
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Matthias De Smet
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bc7002b0c9
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Merge branch 'master' into update/mosdepth
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2022-05-25 19:20:45 +02:00 |
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Matthias De Smet
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72ff2732e3
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add all remaining outputs to mosdepth
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2022-05-25 19:19:39 +02:00 |
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Mahesh Binzer-Panchal
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3d532405a5
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Merge branch 'master' into mash_screen_patch
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2022-05-25 16:51:42 +02:00 |
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SusiJo
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1400f2e683
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fixed tests - mixed chr21 + chr22
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2022-05-25 16:38:30 +02:00 |
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SusiJo
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dd6d838cd7
|
override userEmulation
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2022-05-25 16:37:44 +02:00 |
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Mahesh Binzer-Panchal
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c452f56289
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Patch mash screen
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2022-05-25 12:29:14 +00:00 |
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Jill V. Hagey, PhD
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b1dd1d8a52
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Merge branch 'nf-core:master' into gamma-update
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2022-05-24 19:28:06 -04:00 |
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jvhagey
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127665d27b
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fixed test.yml
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2022-05-24 19:27:09 -04:00 |
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Mahesh Binzer-Panchal
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3d51956b88
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Merge branch 'master' into kat_hist
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2022-05-24 23:10:13 +02:00 |
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jvhagey
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b8aaea7429
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updating paths in test.yml
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2022-05-24 16:27:00 -04:00 |
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jvhagey
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f1fc7fc38e
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adding upzip
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2022-05-24 15:15:07 -04:00 |
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Ramprasad Neethiraj
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c91947f8a1
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Merge branch 'master' into rhocall
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2022-05-24 16:07:55 +02:00 |
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Mahesh Binzer-Panchal
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9a5d6a815b
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Merge branch 'master' into kat_hist
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2022-05-24 15:46:12 +02:00 |
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SusiJo
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3077e4d34c
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Merge branch 'master' into cnvkit/reference
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2022-05-24 15:00:29 +02:00 |
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SusiJo
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8208140d21
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missing meta.id changed
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2022-05-24 14:59:52 +02:00 |
|
Matthias De Smet
|
8381a5e5dd
|
add window test
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2022-05-24 14:43:40 +02:00 |
|
Matthias De Smet
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5bc2d419a9
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fix fail test
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2022-05-24 13:23:00 +02:00 |
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Mahesh Binzer-Panchal
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afb5f226e6
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Merge branch 'master' into kat_hist
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2022-05-24 13:06:31 +02:00 |
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Matthias De Smet
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858cbe80c6
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add must fail test
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2022-05-24 12:43:49 +02:00 |
|
Matthias De Smet
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01fb8851c3
|
mosdept: cram compatiblility
|
2022-05-24 11:47:58 +02:00 |
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Harshil Patel
|
ec141dba08
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Merge branch 'master' into umitools
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2022-05-24 09:23:20 +01:00 |
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Ramprasad Neethiraj
|
b4982ff6e3
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Merge branch 'master' into rhocall
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2022-05-24 09:41:30 +02:00 |
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SusiJo
|
0f0d555f96
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Merge branch 'master' into cnvkit_reference
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2022-05-24 08:03:44 +02:00 |
|
SusiJo
|
0708f343de
|
Merge branch 'master' into cnvkit_bam
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2022-05-24 07:49:51 +02:00 |
|
SusiJo
|
50128b0c86
|
Merge branch 'master' into cnvkit_reference
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2022-05-24 07:49:44 +02:00 |
|
SusiJo
|
1451d62be4
|
rm md5sums for empty files
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2022-05-24 07:38:53 +02:00 |
|
SusiJo
|
63c038ad68
|
Merge branch 'nf-core:master' into cnvkit_bam
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2022-05-24 07:37:24 +02:00 |
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SusiJo
|
b3e2f70651
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Merge branch 'master' into cnvkit/antitarget
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2022-05-24 07:36:07 +02:00 |
|
SusiJo
|
33a72367c6
|
Merge branch 'nf-core:master' into cnvkit_reference
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2022-05-24 07:30:29 +02:00 |
|
Harshil Patel
|
a3e70777ad
|
Fix Conda tests
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2022-05-23 22:39:12 +01:00 |
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Harshil Patel
|
84f02a08a5
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Update umitools/dedup module to make --output-stats optional
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2022-05-23 22:31:09 +01:00 |
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Sateesh Peri
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da0ead705e
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Merge branch 'master' into update/picard
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2022-05-23 13:38:18 -04:00 |
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SusiJo
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8fec7ae321
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added new testdata path
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2022-05-23 19:01:46 +02:00 |
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