Commits · cb1f8e9b0558279ef60913b24b45e8b4ca171ae0 · ESB / ONT_pilot_gitlab · GitLab

10 Nov, 2020 4 commits
- fast5/preproc: mv basecalling to fast5 workflow (issue #103 ) · cb1f8e9b
  Valentina Galata authored Nov 10, 2020
  
  cb1f8e9b
- analysis: mv gene cov from mapping to analysis · 95353429
  Valentina Galata authored Nov 10, 2020
  
  95353429
- assembly: replaced realpath when linking · 4039e29c
  Valentina Galata authored Nov 10, 2020
  
  4039e29c
- conda: simplified requirements · 5b1c69d9
  Valentina Galata authored Nov 10, 2020
  
  5b1c69d9
09 Nov, 2020 2 commits
- workflow: raw data download (issue #102 ) · 7b93a40e
  Valentina Galata authored Nov 09, 2020
  
  7b93a40e
- config: rm ganges · f2abca55
  Valentina Galata authored Nov 09, 2020
  
  f2abca55
05 Nov, 2020 2 commits
- conda: updated ont_fast5_api.yaml · 2d3073a3
  Valentina Galata authored Nov 05, 2020
  
  2d3073a3
- config: updated zymo, gdb and nwc · d988107b
  Valentina Galata authored Nov 05, 2020
  
  d988107b
03 Nov, 2020 3 commits
- config: updated GDB and Zymo · 778fc6a9
  Valentina Galata authored Nov 03, 2020
  
  778fc6a9
- config: updated NWC (issue #88 ) · f54b9e60
  Valentina Galata authored Nov 03, 2020
  
  f54b9e60
- dataset NWC: added configs (issue #88 ) · 64033608
  Valentina Galata authored Nov 03, 2020
  
  64033608
28 Oct, 2020 5 commits
- taxonomy: updated paths to DBs in the rules · 2c89ce8d
  Valentina Galata authored Oct 28, 2020
  
  2c89ce8d
- conda: updated/simplified kaiju/kraken yaml files · f6efcbd5
  Valentina Galata authored Oct 28, 2020
  
  f6efcbd5
- config: updated slurm configs and sbatch scripts for GDB and Zymo (issue #100 ) · 97df27a6
  Valentina Galata authored Oct 28, 2020
  
  97df27a6
- analysis: minor updates · ec1fb3bb
  Valentina Galata authored Oct 28, 2020
  
  ec1fb3bb
- conda: diamond: use older version (0.9.25) (issue #101 ) · a18cd649
  Valentina Galata authored Oct 28, 2020
  
  a18cd649
27 Oct, 2020 2 commits
- config schema: updated (annot/analysis steps, minor changes) · ad1ab96d
  Valentina Galata authored Oct 27, 2020
  
  ad1ab96d
- rm unsed code in workflow/Snakefile · 136c9454
  Valentina Galata authored Oct 27, 2020
  
  136c9454
20 Oct, 2020 5 commits
- conda: downgraded medaka (issue #87 ) · d27f0560
  Valentina Galata authored Oct 20, 2020
  
  d27f0560
- analysis: mv mash rules up in the script · 2fa58388
  Valentina Galata authored Oct 20, 2020
  
  2fa58388
- conda: updated/corrected fastani.yaml (issue #80 ) · 3e1c1492
  Valentina Galata authored Oct 20, 2020
  
  3e1c1492
- analysis: mashmap: fixed typos (issue #95 ) · 4fcfc10c
  Valentina Galata authored Oct 20, 2020
  
  4fcfc10c
- 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