Commits · 3b6ed7edfa5104f829428e6af59ad64e5d9e2c25 · ESB / ONT_pilot_gitlab · GitLab

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Jun 03, 2020
- config/import clean-up: binning · 3b6ed7ed
  Valentina Galata authored 4 years ago
  
  3b6ed7ed
- config/import clean-up: assembly annotation · 4bc62cb2
  Valentina Galata authored 4 years ago
  
  4bc62cb2
- config/import clean-up: assembly annotation · 3ae1c1cc
  Valentina Galata authored 4 years ago
  
  3ae1c1cc
- config/import clean-up: analysis · c574d4e1
  Valentina Galata authored 4 years ago
  
  c574d4e1
- config/import clean-up: analysis · 1e8401ff
  Valentina Galata authored 4 years ago
  
  1e8401ff
- made FAA temp in rgi input rules; other minor changes (issue #29 ) · 2ab9da0b
  Valentina Galata authored 4 years ago
  
  2ab9da0b
- added rgi (issue #29 ) · 5a7350e8
  Valentina Galata authored 4 years ago
  
  5a7350e8
- added .gitignore · 69406c10
  Valentina Galata authored 4 years ago
  
  69406c10
- added plasflow (issue #28 ): includes important updates of config and snakemake files · 32df69ba
  Valentina Galata authored 4 years ago
  
  32df69ba
May 30, 2020
- Update ANALYSIS_RULES · b40e3bfb
  Susheel Busi authored 4 years ago
  
  b40e3bfb
- Update ANALYSIS_RULES · 8b1ece35
  Susheel Busi authored 4 years ago
  
  8b1ece35
- removing the date flag from CASC shell due to errors · aeb752cd
  Susheel Busi authored 4 years ago
  
  aeb752cd
- fixed the path for the minced_CRISPR_output.txt file, and also fixed the CASC issue · e98663ed
  Susheel Busi authored 4 years ago
  
  e98663ed
- included calling the date in the shell · 43c3dfab
  Susheel Busi authored 4 years ago
  
  43c3dfab
- edited the ANALYSIS_RULES for running CASC · 88ef1d4d
  Susheel Busi authored 4 years ago
  
  88ef1d4d
- fixed my (SSB) silly typos - facepalming · 1735ea0d
  Susheel Busi authored 4 years ago
  
  1735ea0d
- edited the to fix the snakemake error - try # 14 million and one · 51c5727f
  Susheel Busi authored 4 years ago
  
  51c5727f
- cleaned up path exporting for rule/ANALYSIS_RULES and added to the config/CONFIG.yaml file · 2717c181
  Susheel Busi authored 4 years ago
  
  2717c181
May 29, 2020
- Update ANALYSIS_RULES · 14b1bfc5
  Susheel Busi authored 4 years ago
  
  14b1bfc5
- Update ANALYSIS_RULES · 66e8779c
  Susheel Busi authored 4 years ago
  
  66e8779c
- Update ANALYSIS_RULES · 0be55987
  Susheel Busi authored 4 years ago
  
  0be55987
- Update ANALYSIS_RULES · 84435595
  Susheel Busi authored 4 years ago
  
  84435595
- Update analysis.smk · 8f6c7117
  Susheel Busi authored 4 years ago
  
  8f6c7117
- Update analysis.smk · 0fd407f7
  Susheel Busi authored 4 years ago
  
  0fd407f7
- Update ANALYSIS_RULES · f2d24d44
  Susheel Busi authored 4 years ago
  
  f2d24d44
- Update ANALYSIS_RULES · 12b0f875
  Susheel Busi authored 4 years ago
  
  12b0f875
- Update ANALYSIS_RULES · 4cc16794
  Susheel Busi authored 4 years ago
  
  4cc16794
- Update ANALYSIS_RULES · 1a1525ac
  Susheel Busi authored 4 years ago
  
  1a1525ac
- Update ANALYSIS_RULES · 6e343c4d
  Susheel Busi authored 4 years ago
  
  6e343c4d
- Update ANALYSIS_RULES · 72ccc18c
  Susheel Busi authored 4 years ago
  
  72ccc18c
May 28, 2020
- added the CRISPR related environments, rules and modified the workflows and... · f0e70006
  Susheel Busi authored 4 years ago
  
  added the CRISPR related environments, rules and modified the workflows and updated_SNAKEFILE accordingly
  f0e70006
- added rules for mappability_index and estimating unique_mapped_reads from BAM files · 9cdb8210
  Susheel Busi authored 4 years ago
  
  9cdb8210
May 27, 2020
- adding the script for coverage plots and the PLOT RULES created by CCL · ecdc09d4
  Susheel Busi authored 4 years ago
  
  ecdc09d4
- updated the SNAKEFILES used for regular analyses · 4f9c606f
  Susheel Busi authored 4 years ago
  
  4f9c606f
- collected miscellaneous files into one folder · 915b2d75
  Susheel Busi authored 4 years ago
  
  915b2d75
- updated the working and workflows SNAKEFILES with additional flag for using... · 9beaa36c
  Susheel Busi authored 4 years ago
  
  updated the working and workflows SNAKEFILES with additional flag for using checkpoints during assembly and annotation
  9beaa36c
May 15, 2020
- updated the overal snakefiles including the with the ANALYSIS_RULES · 1ad79bf6
  Susheel Busi authored 4 years ago
  
  1ad79bf6
- created new ANALYSIS_RULES and workflow for incorporating the cd-hit and quast analyses · 0b5d4048
  Susheel Busi authored 4 years ago
  
  0b5d4048
May 14, 2020
- added the missing config folder · fc05cf06
  Susheel Busi authored 4 years ago
  
  fc05cf06
May 13, 2020
- removed extra scripts folder · 9c976c7c
  Susheel Busi authored 4 years ago
  
  9c976c7c