Commits · a0933e34c55d4bed26510e0fd09fe013441898c1 · biowdl / tasks

Jan 18, 2022
- Add option to assume sort order · a0933e34
  Ruben Vorderman authored 3 years ago
  
  a0933e34
- Update Picard and reevaluate use of intel inflater/defaler · 09b97388
  Ruben Vorderman authored 3 years ago
  
  09b97388
- Set xmx value properly for UmiAwareMarkDuplicatesWithMateCigar · 7b2d86fe
  Ruben Vorderman authored 3 years ago
  
  7b2d86fe
Jan 11, 2022
- Add umiTagName flag · 0a66c48b
  Ruben Vorderman authored 3 years ago
  
  0a66c48b
Jan 04, 2022
- Allow multiple bam inputs · 8ccabed5
  Ruben Vorderman authored 3 years ago
  
  8ccabed5
- Make sure task is consistent · 014d43cc
  Ruben Vorderman authored 3 years ago
  
  014d43cc
Dec 15, 2021
- add umiAwareMarkDuplicate · 9c5ebf6b
  cagaser authored 3 years ago
  
  9c5ebf6b
Nov 19, 2020
- Update versions. · 70b34844
  JasperBoom authored 4 years ago
  
  70b34844
Nov 17, 2020
- Update picard.wdl parameter meta · 3b0874c0
  van den Berg authored 4 years ago
  
  Co-authored-by: Davy Cats <davycats.dc@gmail.com>
  Unverified
  
  3b0874c0
- Add period to end of sentence · 8cc4c073
  van den Berg authored 4 years ago
  
  8cc4c073
- Add parameter meta · d5863eec
  van den Berg authored 4 years ago
  
  d5863eec
Nov 11, 2020
- Update picard. · 4c56f143
  JasperBoom authored 4 years ago
  
  4c56f143
- Fix travis error. · b22cc9f9
  JasperBoom authored 4 years ago
  
  b22cc9f9
- Update picard. · 7dab07f8
  JasperBoom authored 4 years ago
  
  7dab07f8
Nov 10, 2020
- Update more tasks. · b633bd79
  JasperBoom authored 4 years ago
  
  b633bd79
- Add more updates. · aae72ec8
  JasperBoom authored 4 years ago
  
  aae72ec8
Nov 02, 2020
- Add another batch of updated tasks. · 16329034
  JasperBoom authored 4 years ago
  
  16329034
Oct 08, 2020
- Add parameter meta for CollectHsMetrics · 353224aa
  van den Berg authored 4 years ago
  
  353224aa
- Update parameter meta · b6178110
  van den Berg authored 4 years ago
  
  b6178110
- Update picard.wdl · 31bbeddf
  van den Berg authored 4 years ago
  
  Co-authored-by: Jasper <jboom@infernum.nl>
  Unverified
  
  31bbeddf
Oct 07, 2020
- Add HsMetrics and VariantcallingMetrics to picard · a2ae010f
  van den Berg authored 4 years ago
  
  a2ae010f
Jul 28, 2020
- Set compression level to 1 and higher time estimate for mergevcf task · 6eb33c3d
  Ruben Vorderman authored 4 years ago
  
  6eb33c3d
Jul 16, 2020
- Update picard container · 8845e4f5
  Ruben Vorderman authored 4 years ago
  
  8845e4f5
- Add parameter_meta · 4bfae066
  Ruben Vorderman authored 4 years ago
  
  4bfae066
Jul 09, 2020
- Use htsjdk inflaters and deflaters for markduplicates · 8e3788d8
  Ruben Vorderman authored 4 years ago
  
  8e3788d8
Jul 06, 2020
- add parameter_meta · ca368e7e
  Ruben Vorderman authored 4 years ago
  
  ca368e7e
Jul 01, 2020
- make md5 file optional · d29b7e22
  Ruben Vorderman authored 4 years ago
  
  d29b7e22
Jun 30, 2020
- make compression level optional for gather bam files · bbeef08f
  Ruben Vorderman authored 4 years ago
  
  bbeef08f
- increase time for gatherbam · 822e68d9
  Ruben Vorderman authored 4 years ago
  
  822e68d9
- Use memory requirements based on WGS · ef447f28
  Ruben Vorderman authored 4 years ago
  
  ef447f28
Jun 29, 2020
- use validation stringency silent for sort sam · ab72ec3f
  Ruben Vorderman authored 4 years ago
  
  ab72ec3f
Jun 26, 2020
- 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
- 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
- Add sortSam task · 0665c22f
  Ruben Vorderman authored 4 years ago
  
  0665c22f