Commits · ec2bc612c1331e044608c629797076eeedec3187 · biowdl / tasks

Jul 06, 2020
- update changelog · ec2bc612
  Ruben Vorderman authored 4 years ago
  
  ec2bc612
- Merge remote-tracking branch 'origin' into BIOWDL-475 · b107182c
  Ruben Vorderman authored 4 years ago
  
  b107182c
- 2GB per thread is sufficient · d9b05b58
  Ruben Vorderman authored 4 years ago
  
  d9b05b58
- use less memory on bcftools stats. · 46ea0ef3
  Ruben Vorderman authored 4 years ago
  
  46ea0ef3
- Comment on real life use for sambamba markdup · 09772e61
  Ruben Vorderman authored 4 years ago
  
  09772e61
- Only little memory is needed for gatherbqsrreports · 9749968e
  Ruben Vorderman authored 4 years ago
  
  9749968e
- Reduce flagstat memory · a18806aa
  Ruben Vorderman authored 4 years ago
  
  a18806aa
- update haplotypecaller memory · 82bd73ce
  Ruben Vorderman authored 4 years ago
  
  82bd73ce
Jul 03, 2020
- Merge pull request #226 from biowdl/BIOWDL-426 · 6cd572e7
  Jasper authored 4 years ago
  
  BIOWDL-426: Add new tasks to talon.
  Unverified
  
  6cd572e7
- Address last comment. · 68eeeb53
  JasperBoom authored 4 years ago
  
  68eeeb53
- Address comments. · cd18ce6a
  JasperBoom authored 4 years ago
  
  cd18ce6a
Jul 02, 2020
- Update threads and memories. · e921e42f
  JasperBoom authored 4 years ago
  
  e921e42f
- Merge branch 'develop' into BIOWDL-426 · 8ea286df
  Jasper authored 4 years ago
  
  Unverified
  
  8ea286df
- Update tasks. · 71541cbd
  JasperBoom authored 4 years ago
  
  71541cbd
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
- fix samtools merge · 2ec5b8e3
  Ruben Vorderman authored 4 years ago
  
  2ec5b8e3
- Add threads to samtools · e3ba9aa0
  Ruben Vorderman authored 4 years ago
  
  e3ba9aa0
- Use memory requirements based on WGS · ef447f28
  Ruben Vorderman authored 4 years ago
  
  ef447f28
- Use memory estimates from WGS sample · f71d42fd
  Ruben Vorderman authored 4 years ago
  
  f71d42fd
- update sambamba memory requirements and parameter_meta · 187e1277
  Ruben Vorderman authored 4 years ago
  
  187e1277
- 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
- Merge pull request #225 from biowdl/pbmm2 · 71080440
  Jasper authored 4 years ago
  
  Add pbmm2, the PacBio wrapper for minimap2
  Unverified
  
  71080440
- Remove additional thread nonsense · 82e9c135
  Ruben Vorderman authored 4 years ago
  
  82e9c135
- correct additional threads · b81efca4
  Ruben Vorderman authored 4 years ago
  
  b81efca4
- fix sambamba threads · e3a3add7
  Ruben Vorderman authored 4 years ago
  
  e3a3add7
- use validation stringency silent for sort sam · ab72ec3f
  Ruben Vorderman authored 4 years ago
  
  ab72ec3f
- Update scripts · 958aa355
  van den Berg authored 4 years ago
  
  958aa355
- Add bam index to output · 3cbd0cb8
  van den Berg authored 4 years ago
  
  3cbd0cb8
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
- Add new tasks to talon. · e15bcc60
  JasperBoom authored 4 years ago
  
  e15bcc60
- Do not create md5 file by default anymore · 363e90e5
  Ruben Vorderman authored 4 years ago
  
  363e90e5