Commits · 3831097c1e658f83926bbd9277c7f646e6a9d31c · Thomas Weber / Mosaicatcher Update · GitLab

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Jun 26, 2018
- Updated whole README file · 3831097c
  Sascha Meiers authored 6 years ago
  
  3831097c
Jun 21, 2018
- adapt to custom log files · 656d128a
  Sascha Meiers authored 6 years ago
  
  656d128a
- Fix for miscommunication problem between SLURM and snakemake by Jelle Scholtalbers · 68160932
  Sascha Meiers authored 6 years ago
  
  68160932
- adapt cluster times · 14f78d3b
  Sascha Meiers authored 6 years ago
  
  14f78d3b
- fixed weird problem with variable expansion inside awk. · 0d3ca221
  Sascha Meiers authored 6 years ago
  
  0d3ca221
- Merge 'master' (with update normalization tables) into singularity · fb5649a4
  Sascha Meiers authored 6 years ago
  
  fb5649a4
- small updates to prepare singularity for the cluster · fb05af1d
  Sascha Meiers authored 6 years ago
  
  fb05af1d
- Updated normalization to a stricter blacklisting · a3d00010
  Sascha Meiers authored 6 years ago
  
  a3d00010
- Add cluster support via singularity. Not yet fully tested · 5e163603
  Sascha Meiers authored 6 years ago
  
  5e163603
- Merge latest changes from master branch into this one · 3ecce146
  Sascha Meiers authored 6 years ago
  
  3ecce146
Jun 20, 2018
- Changed bash script because a for Loop caused bash 4.4 to hang within Docker · b65fedb8
  Sascha Meiers authored 6 years ago
  
  b65fedb8
- Fixing Dockerfile · 61d4f9eb
  Sascha Meiers authored 6 years ago
  
  61d4f9eb
Jun 19, 2018
- Provide SNV calls by default · 4d2784aa
  Sascha Meiers authored 6 years ago
  
  4d2784aa
- use default parameters of new segmentation · 436847ce
  Sascha Meiers authored 6 years ago
  
  436847ce
- Restructured Dockerfile to utilize layers. Also remove external data... · 0cafafe9
  Sascha Meiers authored 6 years ago
  
  Restructured Dockerfile to utilize layers. Also remove external data (BSgenome.Hsapiens.UCSC.hg38) from image - this has to be provided by the user
  0cafafe9
- Add SNV calls also for singularity image · fe0f4bf8
  Sascha Meiers authored 6 years ago
  
  fe0f4bf8
- Add default VCF files for RPE cell line data · cc1bf0de
  Sascha Meiers authored 6 years ago
  
  cc1bf0de
- Do not install StrandPhaseR! Installation of tools should remain independent... · 04a4fe27
  Sascha Meiers authored 6 years ago
  
  Do not install StrandPhaseR! Installation of tools should remain independent of the workflow description
  04a4fe27
- add new sqrt-based number of segments! · 1feb35a2
  Sascha Meiers authored 6 years ago
  
  1feb35a2
- Add Dockerfile + singularity config · 9a388b09
  Sascha Meiers authored 6 years ago
  
  9a388b09
Jun 18, 2018
- add singularity image. Make reference a parameter instead of input file · d449112a
  Sascha Meiers authored 6 years ago
  
  d449112a
- Fixed package outputs · eb5f7d44
  Sascha Meiers authored 6 years ago
  
  eb5f7d44
Jun 17, 2018
- Fixed small typo · 09197f57
  Sascha Meiers authored 6 years ago
  
  09197f57
- Hopefully fixed bug that messed up `None` bins during counting of observed reads · 5c2e6b1f
  Sascha Meiers authored 6 years ago
  
  5c2e6b1f
- Deprecated warning for old normalization · 1d37914e
  Sascha Meiers authored 6 years ago
  
  1d37914e
- Clean up old entries · 1d52cf23
  Sascha Meiers authored 6 years ago
  
  1d52cf23
Jun 16, 2018
- Unified logging · 58983392
  Sascha Meiers authored 6 years ago
  
  58983392
Jun 15, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 93e8d1c5
  Sascha Meiers authored 6 years ago
  
  93e8d1c5
- Fixed integer problem during mosaiClassifier · 53625fc7
  Sascha Meiers authored 6 years ago
  
  53625fc7
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 81e158c2
  Sascha Meiers authored 6 years ago
  
  81e158c2
- Use more recent SV plot script + do not black list counts based initially · 3ca02902
  Sascha Meiers authored 6 years ago
  
  3ca02902
- Fixing segment coordinates during SV classification · b21cacc7
  Sascha Meiers authored 6 years ago
  
  b21cacc7
- solve off-by-one error in segment breakpoint. Those are reported in 0-based coordinates · 8916a913
  Sascha Meiers authored 6 years ago
  
  8916a913
Jun 14, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 9dd6405d
  Sascha Meiers authored 6 years ago
  
  9dd6405d
- Use more recent version of qc.R · 44c28d26
  Sascha Meiers authored 6 years ago
  
  44c28d26
Jun 13, 2018
- removed analysis folder · 2cf6a35d
  Maryam Ghareghani authored 6 years ago
  
  2cf6a35d
Jun 12, 2018
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 2351e570
  Sascha Meiers authored 6 years ago
  
  2351e570
- Enable new segmentation · 6e5c73f6
  Sascha Meiers authored 6 years ago
  
  6e5c73f6
- Add new way of normalization (right at the start). Remove old one · f07cf7eb
  Sascha Meiers authored 6 years ago
  
  f07cf7eb
- added a directory containing scripts for the analysis of pipeline results · a565b288
  maryamghr authored 6 years ago
  
  a565b288