Commits · e8d9174308fbdfa14d2ccdfc5b1c7859c1d8c03b · SVdetection / cnvpipelines

May 27, 2019
- some comestic changes · e8d91743
  Thomas Faraut authored 5 years ago
  
  e8d91743
Feb 05, 2019
- Duplication support in simulation;Creation of the sample.list containing all... · c1c72ff8
  Mathieu Charles authored 6 years ago
  
  Duplication support in simulation;Creation of the sample.list containing all samples, additionnaly to sample.list.# for batch
  c1c72ff8
Jul 30, 2018
- Remove also fai file · d21d3343
  Floreal Cabanettes authored 6 years ago
  
  d21d3343
- Try fix: remove raw reference once final one is build · a70595d4
  Floreal Cabanettes authored 6 years ago
  
  a70595d4
Jul 18, 2018
- Fix simulation workflow · 83d4c223
  Floreal Cabanettes authored 6 years ago
  
  83d4c223
- Fix bugs due to new chromosomes filtering · b58a72b9
  Floreal Cabanettes authored 6 years ago
  
  b58a72b9
Jul 06, 2018
- - change filter to noFilter (by default filtering is done) · cea5dca8
  Thomas Faraut authored 6 years ago
  
  - simplify gcmaskbed and lcmaskebed (erferencebundle) - Update submodule snakecnv/lib to latest
  cea5dca8
Jul 03, 2018
- Remove message from snk (done in the wrapper · 121d676e
  Floreal Cabanettes authored 6 years ago
  
  121d676e
- Change chromosomes filter: filter by size · cd6f17e8
  Floreal Cabanettes authored 6 years ago
  
  cd6f17e8
- removing natsort and adding a message specifying the chromosomes · dca833d4
  Thomas Faraut authored 6 years ago
  
  dca833d4
Jun 11, 2018
- Fix chromsvmask rule · dc8ee59d
  Floreal Cabanettes authored 6 years ago
  
  dc8ee59d
- Fix PATH for refbundle · a5e12845
  Floreal Cabanettes authored 6 years ago
  
  a5e12845
Jun 08, 2018
- Fix bwa when using referencebundle.snk through popsim.snk · f823ae1a
  Floreal Cabanettes authored 6 years ago
  
  f823ae1a
- Fix chromsmask rule · 0eaf74e7
  Floreal Cabanettes authored 6 years ago
  
  0eaf74e7
Jun 07, 2018
- Add refbundle workflow to the simulation pipeline · 9452d0d0
  Floreal Cabanettes authored 6 years ago
  
  9452d0d0
- Add detection workflow to the simulation pipeline · afbac7cc
  Floreal Cabanettes authored 6 years ago
  
  afbac7cc
May 22, 2018
- adding Z an W and more memory for pindel · 21e2d485
  Thomas Faraut authored 6 years ago
  
  21e2d485
May 09, 2018
- getChomLength bug corrected; pep8 for referencebundle · 06ddcb30
  Thomas Faraut authored 6 years ago
  
  06ddcb30
Apr 27, 2018
- Fix typo · 905c1d62
  Floreal Cabanettes authored 6 years ago
  
  905c1d62
- Add fai requirement to all fasta inputs · 69e29cfd
  Floreal Cabanettes authored 6 years ago
  
  69e29cfd
- Fix samtools index command · d1ed737c
  Floreal Cabanettes authored 6 years ago
  
  d1ed737c
- Fix typo · 7dabd7f3
  Floreal Cabanettes authored 6 years ago
  
  7dabd7f3
- Add missing input file to nstretch · babb2a7a
  Floreal Cabanettes authored 6 years ago
  
  babb2a7a
Apr 24, 2018
- number of threads provided by get_threads · ad784f2f
  Thomas Faraut authored 6 years ago
  
  ad784f2f
Apr 19, 2018
- removing splitchrom · 98993bad
  Thomas Faraut authored 6 years ago
  
  98993bad
- Fix refbundle: make it compatible with the new findNstreches script API · 569ba55c
  Floreal Cabanettes authored 6 years ago
  
  569ba55c
Mar 13, 2018
- restricting reference bundle to valid chromosomes · 4b96c155
  Thomas Faraut authored 7 years ago
  
  4b96c155
- Remove static file · 96f834db
  Floreal Cabanettes authored 7 years ago
  
  96f834db
- Add refbundle to wrapper, Implements #4 · 67945f04
  Floreal Cabanettes authored 7 years ago
  
  67945f04
Mar 12, 2018
- Add species parameter (new) · e63d526f
  Floreal Cabanettes authored 7 years ago
  
  e63d526f
- Remove specie parameter for repeatmasker · 3c2e6b30
  Floreal Cabanettes authored 7 years ago
  
  3c2e6b30
- Add chromosomes filter to reference bundle · ffd9bd46
  Floreal Cabanettes authored 7 years ago
  
  ffd9bd46
- Use picard command instead of jar · a91ee9eb
  Floreal Cabanettes authored 7 years ago
  
  a91ee9eb
- Add rootpath · 0bccc23e
  Floreal Cabanettes authored 7 years ago
  
  0bccc23e
- Get SV_DIR from PATH · 312d0a88
  Floreal Cabanettes authored 7 years ago
  
  312d0a88
- Remove fixed URLs in reference bundel pipeline · 0bfe6562
  Floreal Cabanettes authored 7 years ago
  
  0bfe6562
Feb 16, 2018
- with cnvpipeline · 0a2030f2
  Thomas Faraut authored 7 years ago
  
  0a2030f2
Feb 14, 2018
- adding reference bundle · 9d1429e5
  Thomas Faraut authored 7 years ago
  
  9d1429e5

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