Commits · IMPiris · Laura Denies / PathoFact · GitLab

17 Apr, 2020 8 commits
- conda yaml fix in rules/Universal/Combine_PathoFact · a94704fd
  Valentina Galata authored Apr 17, 2020
  
  a94704fd
- updated scripts/AMR_MGE.R to version from 1fe55556 (+ logging) · 943101e6
  Valentina Galata authored Apr 17, 2020
  
  943101e6
- fixed envs/PlasFlow.yaml to force the installation of PlasFlow from anaconda (update for issue #4 ) · 90b94f7b
  Valentina Galata authored Apr 17, 2020
  
  90b94f7b
- changed envs/PlasFlow.yaml: install from smaegol channel otherwise missing... · 9815552a
  Valentina Galata authored Apr 17, 2020
```
changed envs/PlasFlow.yaml: install from smaegol channel otherwise missing models/ (update for issue #4)
```
  9815552a
- format and xonda yaml fix in AMR rules · 6eeac433
  Valentina Galata authored Apr 17, 2020
  
  6eeac433
- added setup.sh: installation/config steps required after cloning the repo · 6f4134af
  Valentina Galata authored Apr 17, 2020
  
  6f4134af
- updated config.yaml · 2bd614e1
  Valentina Galata authored Apr 17, 2020
  
  2bd614e1
- added DeepARG as submodule · 92ba45d1
  Valentina Galata authored Apr 17, 2020
  
  92ba45d1
16 Apr, 2020 32 commits
- added log to Rscripts and log to associated rules: issue #11 · 231c3c9d
  Valentina Galata authored Apr 16, 2020
  
  231c3c9d
- escaped tab chars in rules: issue #6 · 03f07a6c
  Valentina Galata authored Apr 16, 2020
  
  03f07a6c
- typo and log for seqkit fix: issue #7 · 9d8e3f6a
  Valentina Galata authored Apr 16, 2020
  
  9d8e3f6a
- rm virulence_prediction.py from rules/Virulence as the rules uses version from scripts/: issue #12 · 9147ed22
  Valentina Galata authored Apr 16, 2020
  
  9147ed22
- rm filter.pl from rules/AMR (already in scripts/): issue #12 · 4460f420
  Valentina Galata authored Apr 16, 2020
  
  4460f420
- mv hmm.R: issue #12 · f0462713
  Valentina Galata authored Apr 16, 2020
  
  f0462713
- mv PathoFact.R: issue #12 · 2a016bb9
  Valentina Galata authored Apr 16, 2020
  
  2a016bb9
- mv ownHMM_library.R: issue #12 · 5bf85135
  Valentina Galata authored Apr 16, 2020
  
  5bf85135
- mv AMR_MGE.R: issue #12 · 4ad02d1d
  Valentina Galata authored Apr 16, 2020
  
  4ad02d1d
- added log files to rules w/ CMD: issue #7 · 4d30bf7b
  Valentina Galata authored Apr 16, 2020
  
  4d30bf7b
- format fix in rules/Toxin/Toxin and rules/AMR/Phage · 420210ba
  Valentina Galata authored Apr 16, 2020
  
  420210ba
- format fix in rules/Toxin/Toxin and rules/AMR/Phage · 42ec4a33
  Valentina Galata authored Apr 16, 2020
  
  42ec4a33
- rules/: format/ident fixes, changed/added msg · c5dcf62d
  Valentina Galata authored Apr 16, 2020
  
  c5dcf62d
- format fix in workflows/Combine_PathoFact_workflow · e05500a9
  Valentina Galata authored Apr 16, 2020
  
  e05500a9
- format fix in workflows/AMR_workflow · 8d01b15b
  Valentina Galata authored Apr 16, 2020
  
  8d01b15b
- formatx fix in rules/AMR/AMR · 1c966d7a
  Valentina Galata authored Apr 16, 2020
  
  1c966d7a
- formatx fix in rules/AMR/Combine_MGE_AMR · a704d458
  Valentina Galata authored Apr 16, 2020
  
  a704d458
- format fix in rules/AMR/Phage · 41c66b2a
  Valentina Galata authored Apr 16, 2020
  
  41c66b2a
- formatx fix and conda yaml fix in rules/AMR/Phage · e4681a62
  Valentina Galata authored Apr 16, 2020
  
  e4681a62
- renamed envs/virfinder.yml · 58570ff9
  Valentina Galata authored Apr 16, 2020
  
  58570ff9
- format fix and conda yaml fix in rules/AMR/Plasmid · 7ea4d2b9
  Valentina Galata authored Apr 16, 2020
  
  7ea4d2b9
- renamed AMR.yml to DeepARG.yaml · 739297aa
  Valentina Galata authored Apr 16, 2020
  
  739297aa
- format fix and conda yaml fix in rules/AMR/AMR · d39900df
  Valentina Galata authored Apr 16, 2020
  
  d39900df
- rm tmp file rules/AMR/.AMR_MGE.R.swp · 76c89add
  Valentina Galata authored Apr 16, 2020
  
  76c89add
- workflows/Virulence_workflow · 91cf76de
  Valentina Galata authored Apr 16, 2020
  
  91cf76de
- format fix in rules/Virulence/Virulence_report · b93e3159
  Valentina Galata authored Apr 16, 2020
  
  b93e3159
- format fix rules/Virulence/Virulence · e373488b
  Valentina Galata authored Apr 16, 2020
  
  e373488b
- format fix rules/Virulence/Combine_Virulence_SignalP · 5c71a2fa
  Valentina Galata authored Apr 16, 2020
  
  5c71a2fa
- format fix in Snakefile · 65c1a8d7
  Valentina Galata authored Apr 16, 2020
  
  65c1a8d7
- format fix in rules/Toxin/Toxin · 4db9cd1a
  Valentina Galata authored Apr 16, 2020
  
  4db9cd1a
- format fix and conda yaml fix in rules/Virulence/Virulence · e43ae9f3
  Valentina Galata authored Apr 16, 2020
  
  e43ae9f3
- renamed biopython conda yaml · 4376cc95
  Valentina Galata authored Apr 16, 2020
  
  4376cc95