Commits · f63c43d0ca9810a241ea071ced85279a2289b10b · ESB / ONT_pilot_gitlab · GitLab

20 Oct, 2020 1 commit
- analysis: minor fixes in the rules (comma etc) · f63c43d0
  Valentina Galata authored Oct 20, 2020
  
  f63c43d0
19 Oct, 2020 3 commits
- annotation: updated steps · f30a3e2c
  Valentina Galata authored Oct 19, 2020
  
  f30a3e2c
- conda: updated/cleaned up some yaml files · 8eba8bf1
  Valentina Galata authored Oct 19, 2020
  
  8eba8bf1
- annotation: fixed rgi rule (processed input) · 8ec4797d
  Valentina Galata authored Oct 19, 2020
  
  8ec4797d
16 Oct, 2020 3 commits
- config: GDB update · 2e0757aa
  Valentina Galata authored Oct 16, 2020
  
  2e0757aa
- Snakefile: polishing part of assembly (no if); mapping targets update · bbb9c8e9
  Valentina Galata authored Oct 16, 2020
  
  bbb9c8e9
- mapping: steps/rules update; bedtools yaml update · 429eb725
  Valentina Galata authored Oct 16, 2020
  
  429eb725
15 Oct, 2020 5 commits
- init: allow null value for host_refs for bbmap in config · 51625908
  Valentina Galata authored Oct 15, 2020
  
  51625908
- assembly: polishing: bug fix in polishing_medaka_lr (mult output targets) (issue #87 ) · d73960ca
  Valentina Galata authored Oct 15, 2020
  
  d73960ca
- preproc: fix for having no host refs n config · 50294ba4
  Valentina Galata authored Oct 15, 2020
  
  50294ba4
- config: updated GDB · 6867908f
  Valentina Galata authored Oct 15, 2020
  
  6867908f
- assembly: polishing: fixed a typo in medaka polishing input: raconSR: 5 -> 4 (issue #87 ) · 91819cf9
  Valentina Galata authored Oct 15, 2020
  
  91819cf9
14 Oct, 2020 6 commits
- mapping: rm not used code; one rule for mapping short mg/mt reads; no assembly... · e878ae9d
  Valentina Galata authored Oct 14, 2020
```
mapping: rm not used code; one rule for mapping short mg/mt reads; no assembly wildcard; minor changes
```
  e878ae9d
- assembly: rm not used code · 4167b585
  Valentina Galata authored Oct 14, 2020
  
  4167b585
- preprocessing: put fastqc params in the cmd (instead of config) · b3c04498
  Valentina Galata authored Oct 14, 2020
  
  b3c04498
- conda: updated/simplified medaka and racon yaml files · 23a78326
  Valentina Galata authored Oct 14, 2020
  
  23a78326
- added polishing as a workflow step (issue #87 ) · 8c4eff94
  Valentina Galata authored Oct 14, 2020
  
  8c4eff94
- taxonomy: kraken: rm not used params, add SR params · 328a5fe5
  Valentina Galata authored Oct 14, 2020
  
  328a5fe5
13 Oct, 2020 22 commits
- annotation: added hmmer (kegg) (issue #92 ) · 25a35203
  Valentina Galata authored Oct 13, 2020
  
  25a35203
- annotation: simplified/updated rgi rule · ea5b8f69
  Valentina Galata authored Oct 13, 2020
  
  ea5b8f69
- annotation: replaced ASSEMBLY.FILTERED by ASSEMBLY.POLISHED · 9d5930ad
  Valentina Galata authored Oct 13, 2020
  
  9d5930ad
- annotation: simplified/updated plasflow rule · bff9a295
  Valentina Galata authored Oct 13, 2020
  
  bff9a295
- annotation: added/updated rule messages · f41a2f54
  Valentina Galata authored Oct 13, 2020
  
  f41a2f54
- analysis: added/updated rule messages · c0f03df6
  Valentina Galata authored Oct 13, 2020
  
  c0f03df6
- conda: rm minimap2.yaml · 3a82ade4
  Valentina Galata authored Oct 13, 2020
  
  3a82ade4
- conda: updated some yaml files · c463bddd
  Valentina Galata authored Oct 13, 2020
  
  c463bddd
- conda: added yaml for mashmap (issue #95 ) · 38506b8f
  Valentina Galata authored Oct 13, 2020
  
  38506b8f
- analysis: updated steps · a7fea664
  Valentina Galata authored Oct 13, 2020
  
  a7fea664
- analysis: updated steps · 4c1d8762
  Valentina Galata authored Oct 13, 2020
  
  4c1d8762
- analysis/annotation: mv diamond from annotation to analysis; minor changes · 65053445
  Valentina Galata authored Oct 13, 2020
  
  65053445
- analysis: mashmap: only one comparison (instead of both) (issue #95 ) · cd73fb26
  Valentina Galata authored Oct 13, 2020
  
  cd73fb26
- analysis: mummer/dnadiff: only one comparison (instead of both) (issue #93 ) · 69248818
  Valentina Galata authored Oct 13, 2020
  
  69248818
- analysis: cdhit: only one comparison (instead of both) · 7fee627f
  Valentina Galata authored Oct 13, 2020
  
  7fee627f
- analysis: added diamond (pairwise) (issue #78 ) · f4d2185a
  Valentina Galata authored Oct 13, 2020
  
  f4d2185a
- analysis: minor change · 221ca94b
  Valentina Galata authored Oct 13, 2020
  
  221ca94b
- analysis: rule to rename protens in FAA, updated cdhit input · 3c0c63a1
  Valentina Galata authored Oct 13, 2020
  
  3c0c63a1
- analysis: added mummer/dnadiff (issue #93 ) · 89ca49c5
  Valentina Galata authored Oct 13, 2020
  
  89ca49c5
- analysis: added a forgotten comma · 3895952e
  Valentina Galata authored Oct 13, 2020
  
  3895952e
- analysis: added fastani (issue #80 ) · 448d72a1
  Valentina Galata authored Oct 13, 2020
  
  448d72a1
- analysis: added mashmap (issue #95 ) · 9d4e2111
  Valentina Galata authored Oct 13, 2020
  
  9d4e2111