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 16, 2020
- analysis: contig cov segmentation w/ segclust2d (issue #107 ) · dd9c4808
  Valentina Galata authored 4 years ago
  
  dd9c4808
Nov 13, 2020
- analysis: minor changes (renamed some rules and log files) · b8c24478
  Valentina Galata authored 4 years ago
  
  b8c24478
Nov 10, 2020
- analysis/taxonomy: fixed a bug: proc LR/SR for mash and kraken2 · c4c88b36
  Valentina Galata authored 4 years ago
  
  c4c88b36
- analysis: mv gene cov from mapping to analysis · 95353429
  Valentina Galata authored 4 years ago
  
  95353429
Oct 28, 2020
- analysis: minor updates · ec1fb3bb
  Valentina Galata authored 4 years ago
  
  ec1fb3bb
Oct 20, 2020
- analysis: mv mash rules up in the script · 2fa58388
  Valentina Galata authored 4 years ago
  
  2fa58388
- 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 13, 2020
- analysis: added/updated rule messages · c0f03df6
  Valentina Galata authored 4 years ago
  
  c0f03df6
- analysis/annotation: mv diamond from annotation to analysis; minor changes · 65053445
  Valentina Galata authored 4 years ago
  
  65053445
- analysis: mashmap: only one comparison (instead of both) (issue #95 ) · cd73fb26
  Valentina Galata authored 4 years ago
  
  cd73fb26
- analysis: mummer/dnadiff: only one comparison (instead of both) (issue #93 ) · 69248818
  Valentina Galata authored 4 years ago
  
  69248818
- analysis: cdhit: only one comparison (instead of both) · 7fee627f
  Valentina Galata authored 4 years ago
  
  7fee627f
- analysis: added diamond (pairwise) (issue #78 ) · f4d2185a
  Valentina Galata authored 4 years ago
  
  f4d2185a
- analysis: minor change · 221ca94b
  Valentina Galata authored 4 years ago
  
  221ca94b
- analysis: rule to rename protens in FAA, updated cdhit input · 3c0c63a1
  Valentina Galata authored 4 years ago
  
  3c0c63a1
- analysis: added mummer/dnadiff (issue #93 ) · 89ca49c5
  Valentina Galata authored 4 years ago
  
  89ca49c5
- analysis: added a forgotten comma · 3895952e
  Valentina Galata authored 4 years ago
  
  3895952e
- analysis: added fastani (issue #80 ) · 448d72a1
  Valentina Galata authored 4 years ago
  
  448d72a1
- analysis: added mashmap (issue #95 ) · 9d4e2111
  Valentina Galata authored 4 years ago
  
  9d4e2111
- analysis: quast: minor changes · cb87b5d7
  Valentina Galata authored 4 years ago
  
  cb87b5d7
- analysis: cdhit: simplified code, udpated params (issue #68 ) · 1002a9e8
  Valentina Galata authored 4 years ago
  
  1002a9e8
- analysis: simplified code for mash · dee459c6
  Valentina Galata authored 4 years ago
  
  dee459c6
- analysis: rm unused code for mmseqs2 · b6a340c1
  Valentina Galata authored 4 years ago
  
  b6a340c1
- analysis: rm code for circ contigs · f2edcfbf
  Valentina Galata authored 4 years ago
  
  f2edcfbf
Aug 18, 2020
- mash: rm contig-screen analysis, fixed a bug (not all assemblies included in assembly sketch) · 9df850a2
  Valentina Galata authored 4 years ago
  
  9df850a2
Aug 17, 2020
- fixed paths for some mash rules (issue #79 ) · 31a6605d
  Valentina Galata authored 4 years ago
  
  31a6605d
- cdhit: changed renaming rule (issue #75 ), use '-s2 0.5' (issue #68 ) · 214f07ad
  Valentina Galata authored 4 years ago
  
  214f07ad
Jul 31, 2020
- analysis/report: mash on reads (issue #58 ); minor formatting changes · ce573af6
  Valentina Galata authored 4 years ago
  
  ce573af6
Jul 24, 2020
- cdhit: length diff cutoff (issue #68 ) · c84c44d1
  Valentina Galata authored 4 years ago
  
  c84c44d1
- renamed mash rules · b44dd29d
  Valentina Galata authored 4 years ago
  
  b44dd29d
Jul 23, 2020
- cleanup: replace out/err log by log; changed params for metaquast · 57bd9934
  Valentina Galata authored 4 years ago
  
  57bd9934
Jul 17, 2020
- added mash screen analysis (issue #64 ) · 04c4ddd4
  Valentina Galata authored 4 years ago
  
  04c4ddd4
Jul 10, 2020
- updated mash rules (issue #58 ) · 3f9425a4
  Valentina Galata authored 4 years ago
  
  3f9425a4
Jul 09, 2020
- added mash analysis (issue #58 ) · e08b0f30
  Valentina Galata authored 4 years ago
  
  e08b0f30
- blast-based analysis: find putative circ contigs (issue #53 ) · 1ebb366e
  Valentina Galata authored 4 years ago
  
  1ebb366e
Jul 02, 2020
- workflow: rm partial gene counts rule from analysis (issue #50 ) · 95f70fe7
  Valentina Galata authored 4 years ago
  
  95f70fe7
Jul 01, 2020
- analysis: quast: TSV instead of TXT as target (issue #46 ) · 1fdd1f1e
  Valentina Galata authored 4 years ago
  
  1fdd1f1e