Commits · 757cefb2f5e17b89506f2e3740861ae227cfbfab · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Nov 26, 2020
- analysis: cov seg: more threads (rule), rm short contigs (script) (issue #107 ) · 757cefb2
  Valentina Galata authored 4 years ago
  
  757cefb2
- analysis: cov seg: parallel processing (issue #107 ) · 3f62a5f0
  Valentina Galata authored 4 years ago
  
  3f62a5f0
Nov 24, 2020
- analysis: step: chnaged target declaration for cov · e88649ed
  Valentina Galata authored 4 years ago
  
  e88649ed
- annotation: annotation_hmm_kegg: do not redirect stdout to /dev/null, redirect to log · ecbb5538
  Valentina Galata authored 4 years ago
  
  ecbb5538
- assembly: added lr assembler raven (issue #72 ) · d504bb12
  Valentina Galata authored 4 years ago
  
  d504bb12
Nov 16, 2020
- analysis: contig cov segmentation w/ segclust2d (issue #107 ) · dd9c4808
  Valentina Galata authored 4 years ago
  
  dd9c4808
- conda: YAML for segclust2d (issue #107 ) · 6b271249
  Valentina Galata authored 4 years ago
  
  6b271249
Nov 13, 2020
- analysis: minor changes (renamed some rules and log files) · b8c24478
  Valentina Galata authored 4 years ago
  
  b8c24478
- annotation: fixed a bug in rgi cmd (issue #106 ) · f481e0f9
  Valentina Galata authored 4 years ago
  
  f481e0f9
- preproc: fixed a bug when linking to SR files · 2245d9e2
  Valentina Galata authored 4 years ago
  
  2245d9e2
- tax: added prefix to log file names · da288033
  Valentina Galata authored 4 years ago
  
  da288033
- preproc: fixed a bug in linking LR file, local rules · 2a66ed84
  Valentina Galata authored 4 years ago
  
  2a66ed84
- init: added localrule for linking files · d9ff5696
  Valentina Galata authored 4 years ago
  
  d9ff5696
- assembly: operams cmd update (keep clustering) (issue #104 ) · 304f1933
  Valentina Galata authored 4 years ago
  
  304f1933
- assembly: operams cmd update (issue #104 ), metaspadeshybrid - scaffolds as output (issue #105 ) · 481381f6
  Valentina Galata authored 4 years ago
  
  481381f6
- reprocessing: rm realpath when linking · f4bd2fd6
  Valentina Galata authored 4 years ago
  
  f4bd2fd6
- conda: updated snakemake YAML (requirements) · 517b38bf
  Valentina Galata authored 4 years ago
  
  517b38bf
Nov 11, 2020
- conda: bbmap: added missing '=' between name and version · 140299b9
  Valentina Galata authored 4 years ago
  
  140299b9
Nov 10, 2020
- analysis/taxonomy: fixed a bug: proc LR/SR for mash and kraken2 · c4c88b36
  Valentina Galata authored 4 years ago
  
  c4c88b36
- mapping: fixed a bug: proc LR instead of raw ones for mapping · 041556ee
  Valentina Galata authored 4 years ago
  
  041556ee
- fast5/preproc: mv basecalling to fast5 workflow (issue #103 ) · cb1f8e9b
  Valentina Galata authored 4 years ago
  
  cb1f8e9b
- analysis: mv gene cov from mapping to analysis · 95353429
  Valentina Galata authored 4 years ago
  
  95353429
- assembly: replaced realpath when linking · 4039e29c
  Valentina Galata authored 4 years ago
  
  4039e29c
- conda: simplified requirements · 5b1c69d9
  Valentina Galata authored 4 years ago
  
  5b1c69d9
Oct 28, 2020
- taxonomy: updated paths to DBs in the rules · 2c89ce8d
  Valentina Galata authored 4 years ago
  
  2c89ce8d
- conda: updated/simplified kaiju/kraken yaml files · f6efcbd5
  Valentina Galata authored 4 years ago
  
  f6efcbd5
- analysis: minor updates · ec1fb3bb
  Valentina Galata authored 4 years ago
  
  ec1fb3bb
- conda: diamond: use older version (0.9.25) (issue #101 ) · a18cd649
  Valentina Galata authored 4 years ago
  
  a18cd649
Oct 27, 2020
- rm unsed code in workflow/Snakefile · 136c9454
  Valentina Galata authored 4 years ago
  
  136c9454
Oct 20, 2020
- conda: downgraded medaka (issue #87 ) · d27f0560
  Valentina Galata authored 4 years ago
  
  d27f0560
- analysis: mv mash rules up in the script · 2fa58388
  Valentina Galata authored 4 years ago
  
  2fa58388
- conda: updated/corrected fastani.yaml (issue #80 ) · 3e1c1492
  Valentina Galata authored 4 years ago
  
  3e1c1492
- analysis: mashmap: fixed typos (issue #95 ) · 4fcfc10c
  Valentina Galata authored 4 years ago
  
  4fcfc10c
- analysis: minor fixes in the rules (comma etc) · f63c43d0
  Valentina Galata authored 4 years ago
  
  f63c43d0
Oct 19, 2020
- annotation: updated steps · f30a3e2c
  Valentina Galata authored 4 years ago
  
  f30a3e2c
- conda: updated/cleaned up some yaml files · 8eba8bf1
  Valentina Galata authored 4 years ago
  
  8eba8bf1
- annotation: fixed rgi rule (processed input) · 8ec4797d
  Valentina Galata authored 4 years ago
  
  8ec4797d
Oct 16, 2020
- Snakefile: polishing part of assembly (no if); mapping targets update · bbb9c8e9
  Valentina Galata authored 4 years ago
  
  bbb9c8e9
- mapping: steps/rules update; bedtools yaml update · 429eb725
  Valentina Galata authored 4 years ago
  
  429eb725
Oct 15, 2020
- init: allow null value for host_refs for bbmap in config · 51625908
  Valentina Galata authored 4 years ago
  
  51625908