Commits · 3e7b07970fa1439b3718f8f7d912858c94f657d4 · biowdl / tasks

Jul 13, 2020
- Use more sort threads for alignment if more alignment threads are used · 3e7b0797
  Ruben Vorderman authored 4 years ago
  
  3e7b0797
Jul 06, 2020
- add parameter_meta · ca368e7e
  Ruben Vorderman authored 4 years ago
  
  ca368e7e
- 2GB per thread is sufficient · d9b05b58
  Ruben Vorderman authored 4 years ago
  
  d9b05b58
Jun 30, 2020
- Fix bwakit command · d604025c
  Ruben Vorderman authored 4 years ago
  
  d604025c
- Switch sorting to samtools. Do not index as it is not required for marking duplicates · 2aa28e29
  Ruben Vorderman authored 4 years ago
  
  2aa28e29
Jun 29, 2020
- Remove additional thread nonsense · 82e9c135
  Ruben Vorderman authored 4 years ago
  
  82e9c135
Jun 24, 2020
- correct memory calculation · c6eb077f
  Ruben Vorderman authored 4 years ago
  
  c6eb077f
- update parameter_meta · 4f6bd9ad
  Ruben Vorderman authored 4 years ago
  
  4f6bd9ad
- 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
- 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
May 15, 2020
- fix variable used for time_minutes estimation in bwa · c535d259
  Cats authored 4 years ago
  
  c535d259
May 14, 2020
- adress comments · fa1901c4
  Cats authored 4 years ago
  
  fa1901c4
Apr 08, 2020
- even more time_minutes · 605bba8d
  Cats authored 5 years ago
  
  605bba8d
Apr 06, 2020
- add time_minutes part II · 2c9810f1
  Cats authored 5 years ago
  
  2c9810f1
Mar 26, 2020
- Update bwa.wdl · 310d63da
  Ruben Vorderman authored 5 years ago
  
  Co-Authored-By: Jasper <jboom@infernum.nl>
  310d63da
Mar 25, 2020
- update parameter_meta · 8318491a
  Ruben Vorderman authored 5 years ago
  
  8318491a
- update bwa kit defaults · 2e53d9be
  Ruben Vorderman authored 5 years ago
  
  2e53d9be
Mar 18, 2020
- more threads for BWA by default · 0cedc9aa
  Ruben Vorderman authored 5 years ago
  
  0cedc9aa
Feb 20, 2020
- ensure output dir exists · 368d1264
  Ruben Vorderman authored 5 years ago
  
  368d1264
Feb 11, 2020
- add license headers · 407435d8
  Ruben Vorderman authored 5 years ago
  
  407435d8
Jan 27, 2020
- increase default memory for BWA mem · bf970477
  Cats authored 5 years ago
  
  bf970477
Jan 15, 2020
- add parameter_meta to BWA · febf092d
  Cats authored 5 years ago
  
  febf092d
Dec 10, 2019
- fix SC2046 · 86182571
  Cats authored 5 years ago
  
  86182571
Oct 31, 2019
- add parameter_meta to fastqc · 2fe5710c
  Cats authored 5 years ago
  
  2fe5710c
Oct 01, 2019
- memory Int -> String part 1 · abd99d15
  Cats authored 5 years ago
  
  abd99d15
Sep 25, 2019
- add parameter_meta for bwakit · 71b8929e
  Cats authored 5 years ago
  
  71b8929e
Sep 06, 2019
- cleanup bwa.wdl · 9a15b0e8
  Cats authored 5 years ago
  
  9a15b0e8
Aug 12, 2019
- add option to add .64 to index input for bwakit · cbfd4a3f
  Cats authored 5 years ago
  
  cbfd4a3f
Jul 15, 2019
- fix bwakit Readgroup · 5c0fa32a
  Cats authored 5 years ago
  
  5c0fa32a
Jul 11, 2019
- try postalt "manually" · 537d9c4d
  Cats authored 5 years ago
  
  537d9c4d
Jul 09, 2019
- remove -o pipefail from bwakit · 8391c373
  Cats authored 5 years ago
  
  8391c373
Jul 08, 2019
- add bwakit task · 968e0dd2
  Cats authored 5 years ago
  
  968e0dd2
Jun 24, 2019
- create dockerImage stuff · 4b51b2ff
  Ruben Vorderman authored 5 years ago
  
  4b51b2ff
Jun 06, 2019
- addressed review comments · 0f6459f2
  Ruben Vorderman authored 5 years ago
  
  0f6459f2
Jun 04, 2019
- destroy another struct · 47389236
  Ruben Vorderman authored 5 years ago
  
  47389236