Commits · main · Aviral Jain / SARS CoV2 · GitLab

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Sep 17, 2023
- Delete workflow_sarscov2.png · bef7eb21
  Parisa Golbargtaklimi authored 1 year ago
  
  View commits for tag v1.0 v1.0
  
  bef7eb21
- Upload New File · e3c3274a
  Parisa Golbargtaklimi authored 1 year ago
  
  e3c3274a
- edited a few lines · e3b4fa08
  Aviral Jain authored 1 year ago
  
  e3b4fa08
- Update README.md · 1b253f02
  Aviral Jain authored 1 year ago
  
  1b253f02
- Added download scripts for our samples. · 177dc644
  Aviral Jain authored 1 year ago
  
  177dc644
- Update README.md · ff204a3b
  Aviral Jain authored 1 year ago
  
  ff204a3b
Sep 15, 2023
- Update snakefile_config.yaml · e6a196f9
  Aviral Jain authored 1 year ago
  
  e6a196f9
- updated reports · 58f1448a
  Aviral Jain authored 1 year ago
  
  58f1448a
- Merge branch 'main' of git.computational.bio.uni-giessen.de:ajain/SARS-CoV2 into main · c569b96b
  Aviral Jain authored 1 year ago
  
  c569b96b
- added reports, tree images, updated folder structure · 6fbcb7bc
  Aviral Jain authored 1 year ago
  
  6fbcb7bc
- Update README.md · 2d396804
  Aviral Jain authored 1 year ago
  
  2d396804
- changed scripts folder, added readgroups · e3526318
  Aviral Jain authored 1 year ago
  
  e3526318
- Update README.md · 65316002
  Aviral Jain authored 1 year ago
  
  65316002
- Update README.md · 9d427dc0
  Aviral Jain authored 1 year ago
  
  9d427dc0
- updated steps for snpeff · 871031c3
  Aviral Jain authored 1 year ago
  
  871031c3
- files for snpeff database and rules for snpeff report · f56ea6d0
  Aviral Jain authored 1 year ago
  
  f56ea6d0
- Merge branch 'main' of git.computational.bio.uni-giessen.de:ajain/SARS-CoV2 into main · 213f979f
  Aviral Jain authored 1 year ago
  
  213f979f
- updated Snakefile · 4ef23027
  Aviral Jain authored 1 year ago
  
  4ef23027
Sep 14, 2023
- Update README.md · 5c9ac27d
  Aviral Jain authored 1 year ago
  
  5c9ac27d
- Update README.md · 62b9040c
  Aviral Jain authored 1 year ago
  
  62b9040c
- Update snakefile_config.yaml · 174e40b3
  Aviral Jain authored 1 year ago
  
  174e40b3
- conda_env is updated and final · cb5af005
  Aviral Jain authored 1 year ago
  
  cb5af005
- Update README.md · bedd81ee
  Aviral Jain authored 1 year ago
  
  bedd81ee
- formatted readme · 598e4cd9
  Aviral Jain authored 1 year ago
  
  598e4cd9
- updated readme with all the steps · ec232817
  Aviral Jain authored 1 year ago
  
  ec232817
- scritp für mapping-visualisierung · 1c760162
  Parisa Golbargtaklimi authored 1 year ago
  
  1c760162
Sep 13, 2023
- script für Visualisierung · 1dd24414
  Parisa Golbargtaklimi authored 1 year ago
  
  1dd24414
- Update conda_env_final.yaml · c58e1995
  Parisa Golbargtaklimi authored 1 year ago
  
  c58e1995
- Update conda_env_latest.yaml · 8f4e95b4
  Parisa Golbargtaklimi authored 1 year ago
  
  8f4e95b4
- for phylogeny added bcftools, clustalo, raxml tools and rules · 2c2510bc
  Aviral Jain authored 1 year ago
  
  2c2510bc
Sep 11, 2023
- merged Snakefile from branch dev-gatk · 4f8e1a2c
  Aviral Jain authored 1 year ago
  
  4f8e1a2c
- updated directory structure, read groups infos, snpeff database info · 9815bd91
  Aviral Jain authored 1 year ago
  
  9815bd91
Sep 09, 2023
- added genome name · 5d04873e
  Aviral Jain authored 1 year ago
  
  5d04873e
- Update read group info, to use in AddOrReplaceReadGroups. · ee3c585d
  Aviral Jain authored 1 year ago
  
  ee3c585d
Sep 08, 2023
- added a comment · 4301e291
  Aviral Jain authored 1 year ago
  
  4301e291
- Merge branch 'main' of git.computational.bio.uni-giessen.de:ajain/SARS-CoV2 into main · 4848d56f
  Aviral Jain authored 1 year ago
  
  4848d56f
- refactored the snakefile to reduce config usage, added lofreq to the workflow · 1bbe46f8
  Aviral Jain authored 1 year ago
  
  1bbe46f8
Sep 07, 2023
- updated folder structure and added a script to generate it. · 1ef13222
  Aviral Jain authored 1 year ago
  
  1ef13222
- added latest conda einvironment yaml with picard, lofreq, igv and working snpeff and gatk3. · d24eb51e
  Aviral Jain authored 1 year ago
  
  d24eb51e
Sep 05, 2023
- adding bwa_index and bwa_mem · 53c5617f
  Parisa Golbargtaklimi authored 1 year ago
  
  53c5617f