Commits · c0f66042c88a5a8139917d08cde854dada6dbac6 · Laura Denies / PathoFact

18 Jun, 2020 2 commits
- 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
16 Jun, 2020 1 commit
- remove unnecessary files · cf4b8cf5
  Laura Denies authored Jun 16, 2020
  
  cf4b8cf5
12 Jun, 2020 3 commits
- Merge branch 'PathoFact_updates' of... · f997d34e
  Laura Denies authored Jun 12, 2020
```
Merge branch 'PathoFact_updates' of https://git-r3lab.uni.lu/laura.denies/PathoFact into PathoFact_updates
```
  f997d34e
- update deepARG version and installation process · 7b3ea2ae
  Laura Denies authored Jun 12, 2020
  
  7b3ea2ae
- Removed submodule · 42fbf5c6
  Laura Denies authored Jun 12, 2020
  
  42fbf5c6
11 Jun, 2020 1 commit
- add Prodigal and new split script · 5d05b9d0
  Laura Denies authored Jun 11, 2020
  
  5d05b9d0
09 Jun, 2020 2 commits
- Merge branch 'IMPirisv2' into 'master' · d80a6ad1
  Laura Denies authored Jun 09, 2020
```
Merge master with IMPirisv2

See merge request !2
```
  d80a6ad1
- 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
03 Jun, 2020 2 commits
- Update README.md · fef0c395
  Laura Denies authored Jun 03, 2020
  
  fef0c395
- Update README.md · 61822371
  Laura Denies authored Jun 03, 2020
  
  61822371
20 May, 2020 1 commit
- Update AMR_MGE.R · 96dde8eb
  Laura Denies authored May 20, 2020
  
  96dde8eb
15 May, 2020 4 commits
- Update Snakefile · 357dd754
  Laura Denies authored May 15, 2020
  
  357dd754
- Update config.yaml · 8743db8c
  Laura Denies authored May 15, 2020
  
  8743db8c
- Update Biopython.yaml · a2d12aeb
  Laura Denies authored May 15, 2020
  
  a2d12aeb
- Update DeepVirFinder.yaml · cdfda290
  Laura Denies authored May 15, 2020
  
  cdfda290
30 Apr, 2020 7 commits
- Update README.md · eb4ce0e7
  Laura Denies authored Apr 30, 2020
  
  eb4ce0e7
- Update README.md · 38f6378e
  Laura Denies authored Apr 30, 2020
  
  38f6378e
- Merge branch 'SpringClean' into 'master' · 998ab970
  Laura Denies authored Apr 30, 2020
```
Spring clean

See merge request !1
```
  998ab970
- updated readme · 99f1f93f
  Valentina Galata authored Apr 30, 2020
  
  99f1f93f
- 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
- bug fix in test/Snakefile: rule input based on sub-workflow (related to issue #33 ) · f01fdaba
  Valentina Galata authored Apr 30, 2020
  
  f01fdaba
29 Apr, 2020 3 commits
- updated test/README.md (issue #33 ) · fc161ba3
  Valentina Galata authored Apr 29, 2020
  
  fc161ba3
- added snakemake file to run tests (issue #33 ) · 0ab3c9c0
  Valentina Galata authored Apr 29, 2020
  
  0ab3c9c0
- updated the expected test data output (issue #30 ) · 6e16ecf2
  Valentina Galata authored Apr 29, 2020
  
  6e16ecf2
27 Apr, 2020 4 commits
- updated test/test_config.yaml: incl expected output (issue #30 , #33 ) · fa43828b
  Valentina Galata authored Apr 27, 2020
  
  fa43828b
- changed file paths back (rm test/) in test/set-up.sh (issue #30 ) · db9dfcc4
  Valentina Galata authored Apr 27, 2020
  
  db9dfcc4
- uncommented a cmd line in test/set-up.sh (issue #30 ) · 6af75675
  Valentina Galata authored Apr 27, 2020
  
  6af75675
- fixed bug in test/set-up.sh and updated test/test_sample.contig: excl FASTA... · b793818e
  Valentina Galata authored Apr 27, 2020
```
fixed bug in test/set-up.sh and updated test/test_sample.contig: excl FASTA content from GFF before creating contig table (issue #30)
```
  b793818e
24 Apr, 2020 2 commits
- *.snk to *.smk in files (issue #18 ) · af1f20dc
  Valentina Galata authored Apr 24, 2020
  
  af1f20dc
- *.snk to *.smk (issue #18 ) · 0a7b2929
  Valentina Galata authored Apr 24, 2020
  
  0a7b2929
23 Apr, 2020 6 commits
- added expected test data output (issue #30 ); tracked w/ git lfs · e825caed
  Valentina Galata authored Apr 23, 2020
  
  e825caed
- bug fix: wrong redirect into log file in rules/AMR/Plasmid.snk for filter.pl · 67c3ab83
  Valentina Galata authored Apr 23, 2020
  
  67c3ab83
- 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 1 commit
- added log files to snakemake rules and logging in Rscripts (issue #28 ) · e709e686
  Valentina Galata authored Apr 21, 2020
  
  e709e686