Commits · 73aded297aff15ba0ef185e6a86e4e08b28684e4 · biowdl / tasks

Aug 15, 2019
- account for big vmem usage in mutect · 73aded29
  Ruben Vorderman authored 5 years ago
  
  73aded29
- remove default adapter for cutadapt · a9d987c3
  Ruben Vorderman authored 5 years ago
  
  a9d987c3
- remove default adapter · a5dc8e68
  Ruben Vorderman authored 5 years ago
  
  a5dc8e68
Aug 13, 2019
- Merge pull request #129 from biowdl/BIOWDL-292 · bee1944b
  Ruben Vorderman authored 5 years ago
  
  Update picard
  Unverified
  
  bee1944b
- Merge branch 'develop' into BIOWDL-292 · 293ab12c
  Ruben Vorderman authored 5 years ago
  
  Unverified
  
  293ab12c
Aug 12, 2019
- Merge pull request #131 from biowdl/JasperBoom-patch-dockerImage · 1114d853
  Cats authored 5 years ago
  
  Update dockerTag to dockerImage for common.wdl
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  1114d853
- Merge branch 'develop' into JasperBoom-patch-dockerImage · 2e91b7c5
  JB authored 5 years ago
  
  Unverified
  
  2e91b7c5
- Merge pull request #130 from Amfgcp/fixes-run-shark · 195cb0ed
  Cats authored 5 years ago
  
  update to run in Shark: memory values and no "-o pipefail"
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  195cb0ed
- Add update dockerTag to dockerImage to CHANGELOG.md · b37a58d7
  JB authored 5 years ago
  
  Unverified
  
  b37a58d7
- Update dockerTag to dockerImage · a008c17d
  JB authored 5 years ago
  
  Unverified
  
  a008c17d
- update to run in Shark: memory values and no "-o pipefail" · 0ca15e1e
  António Paulo authored 5 years ago
  
  0ca15e1e
- update changelog · c75f6204
  Ruben Vorderman authored 5 years ago
  
  c75f6204
- update fastqsplitter · a8b78294
  Ruben Vorderman authored 5 years ago
  
  a8b78294
- unify picard · 28344638
  Ruben Vorderman authored 5 years ago
  
  28344638
Aug 06, 2019
- Merge pull request #128 from Amfgcp/m2-gatk4.1.2.0-updates · 36f8f808
  Cats authored 5 years ago
  
  M2 gatk4.1.2.0 updates, CombineVariants and Strelka GT modifying
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  36f8f808
- Merge branch 'm2-gatk4.1.2.0-updates' of https://github.com/Amfgcp/tasks into... · a334fd88
  António Paulo authored 5 years ago
  
  Merge branch 'm2-gatk4.1.2.0-updates' of https://github.com/Amfgcp/tasks into m2-gatk4.1.2.0-updates
  a334fd88
- update legibility for the CombineVariants command · 6221290f
  António Paulo authored 5 years ago
  
  6221290f
- Merge branch 'develop' into m2-gatk4.1.2.0-updates · ed801654
  António Paulo authored 5 years ago
  
  Unverified
  
  ed801654
Aug 05, 2019
- update changelog · 05fda96f
  António Paulo authored 5 years ago
  
  05fda96f
- fix FilterMutectCalls not creating expected output folder · f3888236
  António Paulo authored 5 years ago
  
  f3888236
- fix command according to style guideline · ed6d2cf2
  António Paulo authored 5 years ago
  
  add comment
  ed6d2cf2
- add GATK3 CombineVariants as a task · 03232d6a
  António Paulo authored 5 years ago
  
  03232d6a
- update ModifyStrelka to also add "GT" header · 007ef29d
  António Paulo authored 5 years ago
  
  007ef29d
Aug 04, 2019
- add modify_Strelka as task · 3565efa4
  António Paulo authored 5 years ago
  
  3565efa4
- update changelog · d1522b25
  António Paulo authored 5 years ago
  
  d1522b25
- add GATK FilterMutectCalls as a task · 70ae489e
  António Paulo authored 5 years ago
  
  70ae489e
Aug 02, 2019
- add GATK CalculateContamination as a task · 00aa5fd1
  António Paulo authored 5 years ago
  
  00aa5fd1
- update output file name for GetPileupSummaries GATK task · 781666d6
  António Paulo authored 5 years ago
  
  781666d6
Aug 01, 2019
- add GATK GetPileupSummaries as a task · 789d3240
  António Paulo authored 5 years ago
  
  789d3240
Jul 31, 2019
- update small details related to spacing and inputs · 7f057825
  António Paulo authored 5 years ago
  
  7f057825
- add GATK MergeStats as a task · 61c37d6e
  António Paulo authored 5 years ago
  
  61c37d6e
- add GATK LearnReadOrientationModel as a task · a6f81d20
  António Paulo authored 5 years ago
  
  a6f81d20
- Merge pull request #127 from JasperBoom/develop · 892bcdd1
  Cats authored 5 years ago
  
  Add memory and cores variables to multiqc task.
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  892bcdd1
- Removed cores variable. · 0d1190ca
  JB authored 5 years ago
  
  0d1190ca
- Add memory and cores variables to multiqc task. · 3df31b62
  JB authored 5 years ago
  
  3df31b62
Jul 29, 2019
- Merge pull request #126 from biowdl/BIOWDL-282 · 04ac871e
  Ruben Vorderman authored 5 years ago
  
  Regions no longer required for several GATK tasks
  Unverified
  
  04ac871e
- Merge branch 'develop' into BIOWDL-282 · aeae6ad0
  Ruben Vorderman authored 5 years ago
  
  Unverified
  
  aeae6ad0
- simplify · b9e7dc35
  Ruben Vorderman authored 5 years ago
  
  b9e7dc35
- fix tasks · 7f9c2a90
  Ruben Vorderman authored 5 years ago
  
  7f9c2a90
- Merge pull request #124 from Amfgcp/varDict-filter-flags · 02cf7fc8
  Cats authored 5 years ago
  
  Add flags to varDict filtering script "var2vcf_paired.pl"
  Unverified
  
  02cf7fc8