Commits · 296e4e178d278b575ec20623afd1afb65e1853b5 · Laura Denies / PathoFact · GitLab

23 Apr, 2020 4 commits
- update gitignore: ignore test output in test/ · 296e4e17
  Valentina Galata authored Apr 23, 2020
  
  296e4e17
- replaced scripts/virulence_prediction.py by correct version (issue #31 , related to issue #15 ) · eab5f6ab
  Valentina Galata authored Apr 23, 2020
  
  eab5f6ab
- adjusted paths to snakemake files (added ext. *.snk) (issue #18 ) · 0adaecb2
  Valentina Galata authored Apr 23, 2020
  
  0adaecb2
- created a test data set: FNA, FAA, GFF from IMP3 test data, readme and set-up... · 19640026
  Valentina Galata authored Apr 23, 2020
```
created a test data set: FNA, FAA, GFF from IMP3 test data, readme and set-up script, test config (issue #30)
```
  19640026
21 Apr, 2020 24 commits
- added log files to snakemake rules and logging in Rscripts (issue #28 ) · e709e686
  Valentina Galata authored Apr 21, 2020
  
  e709e686
- cleaned up conda YAML files (issue #23 ) · d0e18ca4
  Valentina Galata authored Apr 21, 2020
  
  d0e18ca4
- HMMER: added YAML, changed path on config.yaml, added conda in rules (issue #22 ) · 8facd498
  Valentina Galata authored Apr 21, 2020
  
  8facd498
- updated config.yaml (issue #21 ) · e18bd311
  Valentina Galata authored Apr 21, 2020
  
  e18bd311
- updated set-up.sh (issue #17 , #19 , #20 , #21 ) · 0092106b
  Valentina Galata authored Apr 21, 2020
  
  0092106b
- rm VirSorter dir in scripts/ (issue #21 ) · a6b1735e
  Valentina Galata authored Apr 21, 2020
  
  a6b1735e
- updated VirStorter.yaml (issue #21 ) · 3f1dde60
  Valentina Galata authored Apr 21, 2020
  
  3f1dde60
- updated config.yaml (issue #20 ) · d33a661b
  Valentina Galata authored Apr 21, 2020
  
  d33a661b
- rm PlasFlow dir in scripts/ (issue #20 ) · b8f1226f
  Valentina Galata authored Apr 21, 2020
  
  b8f1226f
- updated PlasFlow YAML (issue #20 ) · ac53f379
  Valentina Galata authored Apr 21, 2020
  
  ac53f379
- added setup for DeepARG in set-up.sh (issue #19 ) · 78baf4ff
  Valentina Galata authored Apr 21, 2020
  
  78baf4ff
- updated config.yaml (issue #19 ) · 8807fe5b
  Valentina Galata authored Apr 21, 2020
  
  8807fe5b
- updated set-up.sh (issue #17 , #19 ) · 3fd02b28
  Valentina Galata authored Apr 21, 2020
  
  3fd02b28
- rm DeepARG dir in scripts/ (issue #19 ) · 077e8920
  Valentina Galata authored Apr 21, 2020
  
  077e8920
- added submodule DeepARG (issue #19 ) · 00f09d3a
  Valentina Galata authored Apr 21, 2020
  
  00f09d3a
- rm configfile from all snakemake files except Snakefile (issue #25 ) · 9d5a1320
  Valentina Galata authored Apr 21, 2020
  
  9d5a1320
- added workflow parameter to config.yaml and updated Snakefile (issue #24 ) · c2563441
  Valentina Galata authored Apr 21, 2020
  
  c2563441
- added .snk extension to snakemake files in rules/ and workflows/ (issue #18 ) · e0939b4e
  Valentina Galata authored Apr 21, 2020
  
  e0939b4e
- format fix in rules/Virulence (issue #26 ) · e99a228f
  Valentina Galata authored Apr 21, 2020
  
  e99a228f
- format fix in rules/Universal (issue #26 ) · a37ed46c
  Valentina Galata authored Apr 21, 2020
  
  a37ed46c
- format fix in rules/Toxin (issue #26 ) · 02d34030
  Valentina Galata authored Apr 21, 2020
  
  02d34030
- format fix in rules/AMR (issue #26 ) · d0581e48
  Valentina Galata authored Apr 21, 2020
  
  d0581e48
- format fix in workflow files (issue #26 ) · 25774a3f
  Valentina Galata authored Apr 21, 2020
  
  25774a3f
- format fix in Snakefile (issue #26 ) · 086684df
  Valentina Galata authored Apr 21, 2020
  
  086684df
20 Apr, 2020 12 commits
- DeepVirFinder: changed path in config.yaml, deleted dir in scripts/, rm in set-up.sh (issue #17 ) · 616d46cd
  Valentina Galata authored Apr 20, 2020
  
  616d46cd
- added DeepVirFinder as git submodule (issue #17 ) · b56f7fd0
  Valentina Galata authored Apr 20, 2020
  
  b56f7fd0
- added PathoFact.yaml (issue #16 ) · 21ab3f8f
  Valentina Galata authored Apr 20, 2020
  
  21ab3f8f
- adjusted paths to scripts in rules (issue #15 ) · 33756c49
  Valentina Galata authored Apr 20, 2020
  
  33756c49
- rm .snakemake dir in workflows/ (issue #13 ) · 27eb51b0
  Valentina Galata authored Apr 20, 2020
  
  27eb51b0
- mv scripts in rules/ to scripts/ (issue #15 ) · ba3bf94b
  Valentina Galata authored Apr 20, 2020
  
  ba3bf94b
- adjusted paths to YAML files in rules (issue #14 ) · f2d5c20f
  Valentina Galata authored Apr 20, 2020
  
  f2d5c20f
- rm .snakemake dir in rules/Virulence (issue #13 ) · 0d648fe6
  Valentina Galata authored Apr 20, 2020
  
  0d648fe6
- renamed AMR.yml to DeepARG.yaml (issue #14 ); updated gitignore and rm a *.swp file (issue #13 ) · 4c20e060
  Valentina Galata authored Apr 20, 2020
  
  4c20e060
- changed dir and names of conda YAML files (issue #14 ) · 7a0b2a1e
  Valentina Galata authored Apr 20, 2020
  
  7a0b2a1e
- mv conda_environments to envs (issue #14 ) · 8ed38ba0
  Valentina Galata authored Apr 20, 2020
  
  8ed38ba0
- added gitignore (issue #13 ) · 36f530f1
  Valentina Galata authored Apr 20, 2020
  
  36f530f1