Commits · c19f372f948dadd07d2f19660f13d51d6567e08a · Mirrors / biopet.biopet

Jul 14, 2014
- Added variantcalling pipeline based on bam files · c19f372f
  Peter van 't Hof authored 10 years ago
  
  c19f372f
Jul 03, 2014
- Indel realign is now intermediate · bb32c1aa
  Peter van 't Hof authored 10 years ago
  
  bb32c1aa
- Test file changes · b42ce554
  Peter van 't Hof authored 10 years ago
  
  b42ce554
- Added configValue2string · 2057747f
  Peter van 't Hof authored 10 years ago
  
  2057747f
- Added bedtools functions · 9aebd092
  Peter van 't Hof authored 10 years ago
  
  9aebd092
- codestyle fix · e626880a
  Peter van 't Hof authored 10 years ago
  
  e626880a
- Added dependency for bam-metrics · 97cf8080
  Peter van 't Hof authored 10 years ago
  
  97cf8080
- Added dependency for bam-metrics · 7b56eb38
  Peter van 't Hof authored 10 years ago
  
  7b56eb38
- Switched to biopet markduplicates · 349330de
  Peter van 't Hof authored 10 years ago
  
  349330de
- Switched to biopet markduplicates · 9add492d
  Peter van 't Hof authored 10 years ago
  
  9add492d
- First version of working bam-metrics pipeline · 97327078
  Peter van 't Hof authored 10 years ago
  
  97327078
- Added default vmem · 801ac09e
  Peter van 't Hof authored 10 years ago
  
  801ac09e
- Disabled command to report for java jobs · 4b5b6c56
  Peter van 't Hof authored 10 years ago
  
  4b5b6c56
- changed version command to def · ddfac817
  Peter van 't Hof authored 10 years ago
  
  ddfac817
- changed version command to def · c340b559
  Peter van 't Hof authored 10 years ago
  
  c340b559
- Added BiopetFlagstat · 07c486e9
  Peter van 't Hof authored 10 years ago
  
  07c486e9
- Added script for bed to picard interval file · cfe60c25
  Peter van 't Hof authored 10 years ago
  
  cfe60c25
- Added samtools flagstat · 83b6e834
  Peter van 't Hof authored 10 years ago
  
  83b6e834
- Added some picard tools to biopet · fcaea52d
  Peter van 't Hof authored 10 years ago
  
  fcaea52d
Jun 27, 2014
- Removed argonaut · 4deb4b69
  Peter van 't Hof authored 10 years ago
  
  4deb4b69
- Added pipeline template · 102d3f50
  Peter van 't Hof authored 10 years ago
  
  102d3f50
- Added pipeline template · 61f20583
  Peter van 't Hof authored 10 years ago
  
  61f20583
- Added empty pipeline for bam metrics · 7cad5b3f
  Peter van 't Hof authored 10 years ago
  
  7cad5b3f
- Added dependency · e1490bad
  Peter van 't Hof authored 10 years ago
  
  e1490bad
- fix analysisName on Ln · 27db54a8
  Peter van 't Hof authored 10 years ago
  
  27db54a8
- Remove unused import · cafd9cd7
  Peter van 't Hof authored 10 years ago
  
  cafd9cd7
- Added chunking for mapping · b7690fca
  Peter van 't Hof authored 10 years ago
  
  b7690fca
Jun 26, 2014
- fixed call to sub pipeline · 6090fa33
  Peter van 't Hof authored 10 years ago
  
  6090fa33
- Added default flag · bbc21279
  Peter van 't Hof authored 10 years ago
  
  bbc21279
- Added config report · 7d27887a
  Peter van 't Hof authored 10 years ago
  
  7d27887a
- Added config report · cd175ab7
  Peter van 't Hof authored 10 years ago
  
  cd175ab7
- Added config report · 71a74799
  Peter van 't Hof authored 10 years ago
  
  71a74799
- Added stand_call_conf and stand_emit_conf as config option · 40c694ad
  Peter van 't Hof authored 10 years ago
  
  40c694ad
- Added intermediates in creator object · f7f087b2
  Peter van 't Hof authored 10 years ago
  
  f7f087b2
- Added a alternative add function for Intermediate jobs · c4c4c974
  Peter van 't Hof authored 10 years ago
  
  c4c4c974
- Added Intermediate files · cb72d450
  Peter van 't Hof authored 10 years ago
  
  cb72d450
Jun 23, 2014
- pom changes for start of 0.1.3 · 9e9e6022
  Peter van 't Hof authored 10 years ago
  
  9e9e6022
- memory multiples by the number of threads · a779a651
  Peter van 't Hof authored 10 years ago
  
  a779a651
- Added bz2 support · 66dc8af2
  Peter van 't Hof authored 10 years ago
  
  66dc8af2
- Also a class for JavaCommandLineTools · f54fc743
  Peter van 't Hof authored 10 years ago
  
  f54fc743