Commits · fbc7b95956624b01e0e60574e18f6849cc149976 · biowdl / tasks

Jun 26, 2020
- proper threads for sambamba · fbc7b959
  Ruben Vorderman authored 4 years ago
  
  fbc7b959
- sambamba creates index automaticall · 7252022d
  Ruben Vorderman authored 4 years ago
  
  7252022d
- do not require indexes on the markdup task · 8df42e20
  Ruben Vorderman authored 4 years ago
  
  8df42e20
- fix picard optional md5 · 2c4dd54c
  Ruben Vorderman authored 4 years ago
  
  2c4dd54c
- add outputs · caaba597
  Ruben Vorderman authored 4 years ago
  
  caaba597
- add markdup task · 5db2a1f9
  Ruben Vorderman authored 4 years ago
  
  5db2a1f9
- Increase time estimates for sort tasks · ddae5764
  Ruben Vorderman authored 4 years ago
  
  ddae5764
Jun 25, 2020
- Do not create md5 file by default anymore · 363e90e5
  Ruben Vorderman authored 4 years ago
  
  363e90e5
- Picard markduplicates has a default compression of 1 · a7f50e40
  Ruben Vorderman authored 4 years ago
  
  a7f50e40
- update picard · 160ed6f2
  Ruben Vorderman authored 4 years ago
  
  160ed6f2
- Update sortsam task with extra variables · 7b7eb3da
  Ruben Vorderman authored 4 years ago
  
  7b7eb3da
- Actually sort the inputBam, not stdout · 95020710
  Ruben Vorderman authored 4 years ago
  
  95020710
Jun 24, 2020
- Merge branch 'BIOWDL-475' of https://github.com/biowdl/tasks into BIOWDL-475 · 15476e8d
  Ruben Vorderman authored 4 years ago
  
  15476e8d
- use correct memory for sambama · fac254be
  Ruben Vorderman authored 4 years ago
  
  fac254be
- correct memory calculation · c6eb077f
  Ruben Vorderman authored 4 years ago
  
  c6eb077f
- add threads on index as well · 45ffa553
  Ruben Vorderman authored 4 years ago
  
  45ffa553
- Fix sambamba index command in sort · f4a8fac6
  Ruben Vorderman authored 4 years ago
  
  f4a8fac6
- Add sortSam task · 0665c22f
  Ruben Vorderman authored 4 years ago
  
  0665c22f
- update parameter_meta · 4f6bd9ad
  Ruben Vorderman authored 4 years ago
  
  4f6bd9ad
- Make sure samtools uses memory · 99647123
  Ruben Vorderman authored 4 years ago
  
  99647123
- Put sorting back into bwakit task · 5b096cee
  Ruben Vorderman authored 4 years ago
  
  5b096cee
- Revert "Don't sort" · 0cb76481
  Ruben Vorderman authored 4 years ago
  
  This reverts commit b7d9dad9.
  0cb76481
Jun 23, 2020
- use newer more experimental image · 10c023ab
  Ruben Vorderman authored 4 years ago
  
  10c023ab
Jun 22, 2020
- use correct memory estimate · 424178d6
  Ruben Vorderman authored 4 years ago
  
  424178d6
- remove other sorting bits · feae6e79
  Ruben Vorderman authored 4 years ago
  
  feae6e79
- Update samtools sort to also index · 0c9ba9ae
  Ruben Vorderman authored 4 years ago
  
  0c9ba9ae
- Don't sort · b7d9dad9
  Ruben Vorderman authored 4 years ago
  
  b7d9dad9
Jun 19, 2020
- Do not use unnecessary threads · 84f1235c
  Ruben Vorderman authored 4 years ago
  
  84f1235c
Jun 17, 2020
- Merge pull request #224 from biowdl/chunkedscatter · c7e165f9
  Ruben Vorderman authored 4 years ago
  
  Update image for chunked scatter.
  Unverified
  
  c7e165f9
- Update parameter_meta · a0fccc3c
  Ruben Vorderman authored 4 years ago
  
  a0fccc3c
- Update changelog · aea930c6
  Ruben Vorderman authored 4 years ago
  
  aea930c6
- Update image and tasks for chunk scatter · 4402a95d
  Ruben Vorderman authored 4 years ago
  
  4402a95d
Jun 16, 2020
- Merge pull request #223 from biowdl/BIOWDL-471 · 3b583e41
  Ruben Vorderman authored 4 years ago
  
  Updated resource requirements for the RNA-seq pipeline.
  Unverified
  
  3b583e41
- Remove memoryGb from the input section · 5c9b7c83
  Ruben Vorderman authored 4 years ago
  
  5c9b7c83
- add javaxmx parameter_meta · e45b413f
  Ruben Vorderman authored 4 years ago
  
  e45b413f
- Merge branch 'BIOWDL-471' of https://github.com/biowdl/tasks into BIOWDL-471 · 95b19cd5
  Ruben Vorderman authored 4 years ago
  
  95b19cd5
- Update changelog · 88a1d405
  Ruben Vorderman authored 4 years ago
  
  88a1d405
- update gatk varianteval times · f3006d5a
  Ruben Vorderman authored 4 years ago
  
  f3006d5a
- Add scatter-regions to changelog · 5c1625e3
  Ruben Vorderman authored 4 years ago
  
  5c1625e3
- Merge branch 'develop' into BIOWDL-471 · c36bae77
  Ruben Vorderman authored 4 years ago
  
  Unverified
  
  c36bae77