Commits · 96dde8ebf0e3cb33b80a6fe5a8ad0fdff05e5541 · Laura Denies / PathoFact

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 13 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