Commits · 9fe53a1761a67fdbbfd3d70cccdcbdd7a339240c · SVdetection / cnvpipelines

Jan 17, 2019
- bwam in cluster.yaml set to 23h, detect_region_to_exclude modified · 9fe53a17
  Thomas Faraut authored 6 years ago
  
  9fe53a17
Dec 14, 2018
- bug correction · a6854300
  Thomas Faraut authored 6 years ago
  
  a6854300
Dec 12, 2018
- - pindel back to --max_range_index 3 · 9b50863b
  Thomas Faraut authored 6 years ago
  
  - gstrip_preprocess now requires 16Gb of memory
  9b50863b
Dec 05, 2018
- removing izip and pysamstats import · e6a8ad6a
  Thomas Faraut authored 6 years ago
  
  e6a8ad6a
Dec 04, 2018
- - delly ex is now mine · 5225e199
  Thomas Faraut authored 6 years ago
  
  - get_regions to exclude uses not mad
  5225e199
- - delly threads downgraded to 6 · fd66bc96
  Thomas Faraut authored 6 years ago
  
  - genomestrip .Nstrech file not any more required - pindel max_xrange 2 removed - excluded is now preformed for each sample
  fd66bc96
- 36 hours for repeatmasker · 9f69701c
  Thomas Faraut authored 6 years ago
  
  9f69701c
- upgrading lib · b0c65c57
  Thomas Faraut authored 6 years ago
  
  b0c65c57
Oct 23, 2018
- modifying cnvpipeline and delly time · 1c6d32ae
  Thomas Faraut authored 6 years ago
  
  1c6d32ae
- now 8 cores for delly · 24b86bc5
  Thomas Faraut authored 6 years ago
  
  24b86bc5
- removing self._rerun_tools(tools) · b4182d5e
  Thomas Faraut authored 6 years ago
  
  b4182d5e
Oct 19, 2018
- cluster without drmaa fixed · 36551b08
  Thomas Faraut authored 6 years ago
  
  36551b08
- adding batch id to record id in parse · 9408978e
  Thomas Faraut authored 6 years ago
  
  9408978e
- popsim · dafce579
  Thomas Faraut authored 6 years ago
  
  dafce579
- updating snakecnv/lib · fc048fbe
  Thomas Faraut authored 6 years ago
  
  fc048fbe
Oct 05, 2018
- patch for getting chromsomes in get_batches · 272bf2f3
  Thomas Faraut authored 6 years ago
  
  272bf2f3
Sep 27, 2018
- updating the lib submodule · 491fa286
  Thomas Faraut authored 6 years ago
  
  491fa286
- - implementing a pure pysam bacoverage instead of the pysamstats implementation · cd6a9624
  Thomas Faraut authored 6 years ago
  
  - window width for the detection of high coverage is now 500bp - simplifying gzip of pindel files
  cd6a9624
Aug 24, 2018
- Update summary ipynb · 13fc368c
  Floreal Cabanettes authored 6 years ago
  
  13fc368c
- Fix summary rule · 2fedb544
  Floreal Cabanettes authored 6 years ago
  
  2fedb544
- Fix input · c3d1baaa
  Floreal Cabanettes authored 6 years ago
  
  c3d1baaa
- Fix variable name · c11772ca
  Floreal Cabanettes authored 6 years ago
  
  c11772ca
- Fix syntac · d1f9176a
  Floreal Cabanettes authored 6 years ago
  
  d1f9176a
- Add summary · a54b7305
  Floreal Cabanettes authored 6 years ago
  
  a54b7305
Aug 23, 2018
- Fix if dry run done before run · 965d4e7e
  Floreal Cabanettes authored 6 years ago
  
  965d4e7e
- Easy dry run if only 1 batch · ee8cb8b6
  Floreal Cabanettes authored 6 years ago
  
  ee8cb8b6
- Upgrade popsim submodule · 41c767ef
  Floreal Cabanettes authored 6 years ago
  
  41c767ef
- Merge branch 'master' of forgemia.inra.fr:genotoul-bioinfo/cnvpipelines · 9ea1b75b
  Thomas Faraut authored 6 years ago
  
  9ea1b75b
- upgrading lib · 5923e4f3
  Thomas Faraut authored 6 years ago
  
  5923e4f3
Aug 22, 2018
- Allow several RG tags if all have the same SM flag · 9a475021
  Floreal Cabanettes authored 6 years ago
  
  9a475021
- Fix delete of wdir on dry run for detection pipeline · 1074a0f9
  Floreal Cabanettes authored 6 years ago
  
  1074a0f9
- Remove done files at run detection twice · 5f725e3e
  Floreal Cabanettes authored 6 years ago
  
  5f725e3e
- Fix python code · bb7923b3
  Floreal Cabanettes authored 6 years ago
  
  bb7923b3
Aug 21, 2018
- test · 6ba7f9d6
  Thomas Faraut authored 6 years ago
  
  6ba7f9d6
- . and PASS are now PASS · 7919032e
  Thomas Faraut authored 6 years ago
  
  7919032e
- Merge branch 'master' of forgemia.inra.fr:genotoul-bioinfo/cnvpipelines · 1bc65f06
  Thomas Faraut authored 6 years ago
  
  1bc65f06
Aug 20, 2018
- Fix message · 5fc613df
  Floreal Cabanettes authored 6 years ago
  
  5fc613df
- Fix error code · ed416645
  Floreal Cabanettes authored 6 years ago
  
  ed416645
- Disallow run twice with a different batch size · c83ba8bd
  Floreal Cabanettes authored 6 years ago
  
  c83ba8bd
- Run a job twice not allowed for simulation. Run a job twice check wf_type compatibility · 879faae0
  Floreal Cabanettes authored 6 years ago
  
  879faae0