Commits · 9cdb8210c0fa35100abd88403781c5f4afa68919 · ESB / ONT_pilot_gitlab

May 28, 2020
- 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
- Add new file · 9e902c4b
  Susheel Busi authored 4 years ago
  
  9e902c4b
- Add new file · 125b79a7
  Susheel Busi authored 4 years ago
  
  125b79a7
- Add new file · 9431e606
  Susheel Busi authored 4 years ago
  
  9431e606
- fixed the metaspades overlap with mmseq plotting · b97e0104
  Susheel Busi authored 4 years ago
  
  b97e0104
- fixed the mmseq plotting scripts · 59f0e8b1
  Susheel Busi authored 4 years ago
  
  59f0e8b1
May 12, 2020
- updating the repository · 0caae0a3
  Susheel Busi authored 4 years ago
  
  0caae0a3
- fixed awk error in the mmseq prepare files script · 73dd1bc8
  Susheel Busi authored 4 years ago
  
  73dd1bc8
- included scripts for mmseq plotting with metaspades · f37ddcf7
  Susheel Busi authored 4 years ago
  
  f37ddcf7
- updated mmseq plot scripts - working finally · 87b28001
  Susheel Busi authored 4 years ago
  
  87b28001
- updated checkpoint rules · edb39754
  Susheel Busi authored 4 years ago
  
  edb39754
- updated rules and workflows for running assembly with spades and mmseq comparisons · 10ce73e6
  Susheel Busi authored 4 years ago
  
  10ce73e6
May 11, 2020
- snakefile with the checkpoint workflows · 15a986b6
  Susheel Busi authored 4 years ago
  
  15a986b6
- updated checkpoint workflow · a016d9eb
  Susheel Busi authored 4 years ago
  
  a016d9eb
- updated checkpoint rules · c86339aa
  Susheel Busi authored 4 years ago
  
  c86339aa
May 09, 2020
- Update BINNING_RULES · dc87ff4f
  Susheel Busi authored 4 years ago
  
  dc87ff4f
- updated MMSEQ and MAPPING rules to avoid missing input exceptions and for the mmseq error · e03a3502
  Susheel Busi authored 4 years ago
  
  e03a3502
- updated the config file with mmseq paths to local installation due to - 'results2rbh died error' · 0c4653c1
  Susheel Busi authored 4 years ago
  
  0c4653c1
- Update MMSEQ_RULES · 03e53250
  Susheel Busi authored 4 years ago
  
  03e53250
- Update MMSEQ_RULES · 75684db1
  Susheel Busi authored 4 years ago
  
  75684db1
- Update mapping.smk · 539ac4d6
  Susheel Busi authored 4 years ago
  
  539ac4d6
- Update MAPPING_RULES · 90dc7d11
  Susheel Busi authored 4 years ago
  
  90dc7d11
- Update MMSEQ_RULES · fd8f8cd8
  Susheel Busi authored 4 years ago
  
  fd8f8cd8
May 08, 2020
- Update diamond.yaml · d01b33cc
  Susheel Busi authored 4 years ago
  
  d01b33cc
May 07, 2020
- Merge branch '2019_GDB' into 'master' · ee98b17e
  Susheel Busi authored 4 years ago
  
  changes for 2019 data See merge request susheel.busi/ont_pilot_gitlab!66
  ee98b17e
- changes for 2019 data · 588ce7ed
  Susheel Busi authored 4 years ago
  
  588ce7ed
May 06, 2020
- Merge branch '2019_GDB' into 'master' · 539d7f74
  Susheel Busi authored 4 years ago
  
  updated configs, rules, etc. for 2019_GDB ONT analyses See merge request susheel.busi/ont_pilot_gitlab!65
  539d7f74
- updated configs, rules, etc. for 2019_GDB ONT analyses · e6afa39b
  Susheel Busi authored 4 years ago
  
  e6afa39b
May 01, 2020
- minor changes · f286f75b
  Susheel Busi authored 4 years ago
  
  f286f75b
- Add new file · b143371e
  Susheel Busi authored 4 years ago
  
  b143371e
- Merge branch 'work' into 'master' · 9444376f
  Susheel Busi authored 4 years ago
  
  cleaner snakefile for workflow See merge request susheel.busi/ont_pilot_gitlab!64
  9444376f
- cleaner snakefile for workflow · d2bb2244
  Susheel Busi authored 4 years ago
  
  d2bb2244