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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de88adc926
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Standardise parameters (no tests yet until realigntarget creator ready)
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2022-06-02 20:35:34 +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 Fellows Yates
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599b264280
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Standaridse parameters
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2022-06-02 20:27:16 +02:00 |
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James A. Fellows Yates
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b1edcc6e94
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Update modules/gatk/realignertargetcreator/main.nf
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2022-06-02 20:26:09 +02:00 |
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James A. Fellows Yates
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43ef3841d1
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remove duplciate path
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2022-06-02 20:25:12 +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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James Fellows Yates
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28101149b6
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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 20:24:17 +02:00 |
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James Fellows Yates
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14c63f9ccc
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Changes after review
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2022-06-02 20:24:14 +02:00 |
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nvnieuwk
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fcc186d717
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Merge pull request #1728 from nvnieuwk/add-intervals-to-calibratedragstrmodel
add intervals to gatk4/calibratedragstrmodel
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2022-06-02 16:28:25 +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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b028e57588
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Merge branch 'add-intervals-to-calibratedragstrmodel' of github.com:nvnieuwk/modules into add-intervals-to-calibratedragstrmodel
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2022-06-02 16:24:06 +02:00 |
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Nicolas Vannieuwkerke
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f3c0107fa2
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added optional to intervals
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2022-06-02 16:24:03 +02:00 |
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SusiJo
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efc1e1bb71
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rm line
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 16:23:18 +02:00 |
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SusiJo
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44daa5d687
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update prefix
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
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2022-06-02 16:23:09 +02:00 |
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nvnieuwk
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897de827ee
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Merge branch 'master' into add-intervals-to-calibratedragstrmodel
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2022-06-02 16:20:41 +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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Maxime U. Garcia
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3adb54c606
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Merge pull request #1727 from maxulysse/master_ensemblvep
update VEP version + cache
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2022-06-02 16:15:31 +02:00 |
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MaxUlysse
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b623ff5d27
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fix comments
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2022-06-02 16:11:45 +02:00 |
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MaxUlysse
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bc0f52bcd3
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fix cache version
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2022-06-02 16:11:11 +02:00 |
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MaxUlysse
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046fa39582
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update VEP version + cache
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2022-06-02 16:09:09 +02:00 |
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nvnieuwk
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59ce1ec348
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Merge pull request #1725 from nvnieuwk/add-dragstrmodel-to-haplotypecaller
add dragstr model to haplotypecaller
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2022-06-02 14:31:53 +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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5447395975
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Merge pull request #1724 from nvnieuwk/new-module-gatk4/CalibrateDragstrModel
new module gatk4/calibratedragstrmodel
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2022-06-02 13:49:44 +02:00 |
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Matthias De Smet
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db0dc81b81
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Merge branch 'master' into bump/picard
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2022-06-02 13:49:03 +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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Matthias De Smet
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22885ce687
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Merge pull request #1723 from matthdsm/update/untar
fix untar output dir
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2022-06-02 13:42:46 +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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nvnieuwk
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3a49b82863
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Update modules/gatk4/calibratedragstrmodel/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
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2022-06-02 13:39:44 +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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SusiJo
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1c33eeb348
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Merge pull request #1719 from SusiJo/cnvkit_bam
Adjusted CNVKIT/BATCH for germline mode
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2022-06-02 13:36:39 +02:00 |
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Nicolas Vannieuwkerke
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631bf7749a
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Merge branch 'new-module-gatk4/CalibrateDragstrModel' of github.com:nvnieuwk/modules into new-module-gatk4/CalibrateDragstrModel
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2022-06-02 13:22:57 +02:00 |
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Nicolas Vannieuwkerke
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d3874bbae9
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linting
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2022-06-02 13:22:55 +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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45f3795670
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Merge branch 'master' into bump/picard
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2022-06-02 11:33:26 +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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3294def3fd
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Merge pull request #1722 from SusiJo/deeptools_samtools
Adjust deeptools/bamcoverage with new mulled container
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2022-06-02 10:50:05 +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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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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