Commits · 804a5f501051318476a7c038caaa76c1ab61288d · Laura Denies / PathoFact

21 Jul, 2020 2 commits
- update test module · 804a5f50
  Laura Denies authored Jul 21, 2020
  
  804a5f50
- failsafe empty files · 72cf8aea
  Laura Denies authored Jul 21, 2020
  
  72cf8aea
06 Jul, 2020 1 commit
- update signalp rules · 72f0b27f
  Laura Denies authored Jul 06, 2020
  
  72f0b27f
22 Jun, 2020 5 commits
- make intermediate files temp · 1a2c8a22
  Laura Denies authored Jun 22, 2020
  
  1a2c8a22
- update PathoFact report · 97113017
  Laura Denies authored Jun 22, 2020
  
  97113017
- adjusted virulence report to include SignalP v5.0 · a09f2eaf
  Laura Denies authored Jun 22, 2020
  
  a09f2eaf
- update HMM virulence prediction report · 03b526bc
  Laura Denies authored Jun 22, 2020
  
  03b526bc
- update Toxin_report with SignalP v5.0 results · 850f0c34
  Laura Denies authored Jun 22, 2020
  
  850f0c34
19 Jun, 2020 1 commit
- updated signalp to v5.0 · 4e54bc02
  Laura Denies authored Jun 19, 2020
  
  4e54bc02
18 Jun, 2020 4 commits
- Updated AMR workflow: combine results · 21195b19
  Laura Denies authored Jun 18, 2020
  
  21195b19
- incorporated failsafe for empty VIRSorter prediction files · 96415bbc
  Laura Denies authored Jun 18, 2020
  
  96415bbc
- adjusted ORFs ID translation · c0f66042
  Laura Denies authored Jun 18, 2020
  
  c0f66042
- Include MOB_suite for Plasmid prediction | modify MGE prediction · 01b6b60d
  Laura Denies authored Jun 18, 2020
  
  01b6b60d
17 Jun, 2020 1 commit
- Integrate RGI within AMR workflow · 223aa6a5
  Laura Denies authored Jun 17, 2020
  
  223aa6a5
12 Jun, 2020 1 commit
- update deepARG version and installation process · 7b3ea2ae
  Laura Denies authored Jun 12, 2020
  
  7b3ea2ae
11 Jun, 2020 1 commit
- add Prodigal and new split script · 5d05b9d0
  Laura Denies authored Jun 11, 2020
  
  5d05b9d0
09 Jun, 2020 1 commit
- adjusted the rules to include mem and runtime for cluster config: updated... · 6589efab
  Valentina Galata authored Jun 09, 2020 and Laura Denies committed Jun 09, 2020
```
adjusted the rules to include mem and runtime for cluster config: updated configs; added slurm config; added cluster scripts; other minor updates
```
  6589efab
30 Apr, 2020 2 commits
- replaced index by name when accessing snakemake variables (issue #29 ) · 46961fc8
  Valentina Galata authored Apr 30, 2020
  
  46961fc8
- escaping tabs in rule cmds properly (issue #32 ) · 0ba12560
  Valentina Galata authored Apr 30, 2020
  
  0ba12560
24 Apr, 2020 1 commit
- *.snk to *.smk (issue #18 ) · 0a7b2929
  Valentina Galata authored Apr 24, 2020
  
  0a7b2929
23 Apr, 2020 1 commit
- bug fix: wrong redirect into log file in rules/AMR/Plasmid.snk for filter.pl · 67c3ab83
  Valentina Galata authored Apr 23, 2020
  
  67c3ab83
21 Apr, 2020 8 commits
- added log files to snakemake rules and logging in Rscripts (issue #28 ) · e709e686
  Valentina Galata authored Apr 21, 2020
  
  e709e686
- HMMER: added YAML, changed path on config.yaml, added conda in rules (issue #22 ) · 8facd498
  Valentina Galata authored Apr 21, 2020
  
  8facd498
- rm configfile from all snakemake files except Snakefile (issue #25 ) · 9d5a1320
  Valentina Galata authored Apr 21, 2020
  
  9d5a1320
- 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
20 Apr, 2020 5 commits
- adjusted paths to scripts in rules (issue #15 ) · 33756c49
  Valentina Galata authored Apr 20, 2020
  
  33756c49
- 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
17 Apr, 2020 1 commit
- Updated AMR_MGE.R · 1fe55556
  Laura Denies authored Apr 17, 2020
  
  1fe55556
24 Mar, 2020 3 commits
- Update PathoFact.R · 8af093ef
  Laura Denies authored Mar 24, 2020
  
  8af093ef
- Update AMR_MGE.R · 9689fc84
  Laura Denies authored Mar 24, 2020
  
  9689fc84
- Update ownHMM_library.R · 78d1317c
  Laura Denies authored Mar 24, 2020
  
  78d1317c
12 Feb, 2020 1 commit
- Update AMR_MGE.R · c33869cf
  Laura Denies authored Feb 12, 2020
  
  c33869cf
22 Jan, 2020 1 commit
- Update ViruTox.R · cf4d6d61
  Laura Denies authored Jan 22, 2020
  
  cf4d6d61