Commits · master · eortega / coevolution

10 Apr, 2020 1 commit
- Prepare to work in local computer · 2109733d
  eortega authored Apr 10, 2020
  
  2109733d
27 Mar, 2020 1 commit
- Add bacteria folder · d58c8843
  eortega authored Mar 27, 2020
  
  d58c8843
28 Feb, 2020 1 commit
- Corrected path to fasta file in scripts/get_PAM.py · 3dea05af
  eortega authored Feb 28, 2020
  
  3dea05af
21 Feb, 2020 3 commits
- Updated readme for get_PAM.py and update_ref_genome.py · cdda5692
  eortega authored Feb 21, 2020
  
  cdda5692
- Removed older versions of scripts · c4ec68b0
  Enrique Ortega enrique.ortega@cefe.cnrs.fr authored Feb 21, 2020
  
  c4ec68b0
- Added script to detect PAMs and to make a consensus reference with T0-WT · b0f115f0
  eortega authored Feb 21, 2020
  
  b0f115f0
16 Jan, 2020 2 commits
- added samtools flagstat only mapped · 8b70093a
  eortega authored Jan 16, 2020
  
  8b70093a
- corrected path management in scripts/04_snpcalling.sh typos correction · 80a64aa1
  eortega authored Jan 16, 2020
  
  80a64aa1
14 Jan, 2020 9 commits
- Merge branch 'Check_run_post_restructure' into 'master' · 3cb49c4a
  eortega authored Jan 14, 2020
```
Updated comments on scripts/procedure.sh

See merge request !6
```
  3cb49c4a
- Updated comments on scripts/procedure.sh · c954934b
  eortega authored Jan 14, 2020
  
  c954934b
- Merge branch 'Check_run_post_restructure' into 'master' · 300e8e7f
  eortega authored Jan 14, 2020
```
Check run post restructure

See merge request !5
```
  300e8e7f
- Made comments more explicit · e54f91ae
  eortega authored Jan 14, 2020
  
  e54f91ae
- corrected scripts/03_mapping.sh and scripts/04_snpcalling.sh. fixed... · 2ee341c0
  eortega authored Jan 14, 2020
```
corrected scripts/03_mapping.sh and scripts/04_snpcalling.sh. fixed scripts/procedure.sh according to new structure
```
  2ee341c0
- Merge branch 'Check_run_post_restructure' into 'master' · fe922c14
  eortega authored Jan 14, 2020
```
Updated script/02_trimm_and_clean and adjusted scripts/procedures.sh accordingly

See merge request !4
```
  fe922c14
- Updated script/02_trimm_and_clean and adjusted scripts/procedures.sh accordingly · 859f779c
  eortega authored Jan 14, 2020
  
  859f779c
- Merge branch 'Check_run_post_restructure' into 'master' · 9f181196
  eortega authored Jan 14, 2020
```
Check run post restructure

See merge request !3
```
  9f181196
- scripts/procedure.sh updated and scripts/00_create_py_env.sh and... · a0e243ef
  eortega authored Jan 14, 2020
```
scripts/procedure.sh updated and scripts/00_create_py_env.sh and 01_quality_check.sh updated to new architecture
```
  a0e243ef
13 Jan, 2020 1 commit
- Separate raw data in groups and updated README.md accordingly · c4017642
  eortega authored Jan 13, 2020
  
  c4017642
10 Jan, 2020 7 commits
- Last description of reminding files. · 0b4d4c6c
  eortega authored Jan 10, 2020
  
  0b4d4c6c
- scripts/README.md all scripts have been described · 49794d53
  eortega authored Jan 10, 2020
  
  49794d53
- Corrected hard written paths on script 04 and updated README.md · fa2f815a
  eortega authored Jan 10, 2020
  
  fa2f815a
- deleted README.txt · 4987e496
  eortega authored Jan 10, 2020
  
  4987e496
- Corrected 02 and 03's input argument corrected. Commented 3 scripts in the readme. · bfc05ce5
  eortega authored Jan 10, 2020
  
  bfc05ce5
- Coding stye and list of files added to scripts/README.md. README.txt is now README.md · 6003a162
  eortega authored Jan 10, 2020
  
  6003a162
- Added scripts/README.txt · 5c73fc0b
  eortega authored Jan 10, 2020
  
  5c73fc0b
08 Jan, 2020 2 commits
- Merge branch 'freq_matrix_overwritten' into 'master' · e8252b78
  eortega authored Jan 08, 2020
```
Added installer for virtual env

See merge request !2
```
  e8252b78
- Added installer for virtual env · 7ad56d05
  eortega authored Jan 08, 2020
  
  7ad56d05
16 Dec, 2019 8 commits
- Merge branch 'freq_matrix_overwritten' into 'master' · 0a8d8e8b
  eortega authored Dec 16, 2019
```
Freq matrix overwritten

See merge request !1
```
  0a8d8e8b
- git rm commited log files · 35d2e9a6
  eortega authored Dec 16, 2019
  
  35d2e9a6
- Updated .gitignore. added *.log · 52664453
  eortega authored Dec 16, 2019
  
  52664453
- Update .gitignore. removed steps/ from .gitignore, added *.html. Allowing to save steps/README.txt · 1cb43e44
  eortega authored Dec 16, 2019
  
  1cb43e44
- Reordered all data. Steps folder created with outputs from the different steps · ca30ae22
  eortega authored Dec 16, 2019
  
  ca30ae22
- update .gitignore not to save the steps/ directory · f106b590
  eortega authored Dec 16, 2019
  
  f106b590
- Added instructions in scripts/vcf_parser3.py in a new branch · c10148cd
  eortega authored Dec 16, 2019
  
  c10148cd
- Initial commit · 0a8b3f0a
  eortega authored Dec 16, 2019
  
  0a8b3f0a