Commits · 4167b585935b17fd3f7c5a1dccf50422a79b3fc6 · ESB / ONT_pilot_gitlab · GitLab

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Oct 14, 2020
- assembly: rm not used code · 4167b585
  Valentina Galata authored 4 years ago
  
  4167b585
- preprocessing: put fastqc params in the cmd (instead of config) · b3c04498
  Valentina Galata authored 4 years ago
  
  b3c04498
- conda: updated/simplified medaka and racon yaml files · 23a78326
  Valentina Galata authored 4 years ago
  
  23a78326
- added polishing as a workflow step (issue #87 ) · 8c4eff94
  Valentina Galata authored 4 years ago
  
  8c4eff94
- taxonomy: kraken: rm not used params, add SR params · 328a5fe5
  Valentina Galata authored 4 years ago
  
  328a5fe5
Oct 13, 2020
- annotation: added hmmer (kegg) (issue #92 ) · 25a35203
  Valentina Galata authored 4 years ago
  
  25a35203
- annotation: simplified/updated rgi rule · ea5b8f69
  Valentina Galata authored 4 years ago
  
  ea5b8f69
- annotation: replaced ASSEMBLY.FILTERED by ASSEMBLY.POLISHED · 9d5930ad
  Valentina Galata authored 4 years ago
  
  9d5930ad
- annotation: simplified/updated plasflow rule · bff9a295
  Valentina Galata authored 4 years ago
  
  bff9a295
- annotation: added/updated rule messages · f41a2f54
  Valentina Galata authored 4 years ago
  
  f41a2f54
- analysis: added/updated rule messages · c0f03df6
  Valentina Galata authored 4 years ago
  
  c0f03df6
- conda: rm minimap2.yaml · 3a82ade4
  Valentina Galata authored 4 years ago
  
  3a82ade4
- conda: updated some yaml files · c463bddd
  Valentina Galata authored 4 years ago
  
  c463bddd
- conda: added yaml for mashmap (issue #95 ) · 38506b8f
  Valentina Galata authored 4 years ago
  
  38506b8f
- analysis: updated steps · a7fea664
  Valentina Galata authored 4 years ago
  
  a7fea664
- analysis: updated steps · 4c1d8762
  Valentina Galata authored 4 years ago
  
  4c1d8762
- 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
- setup: updated operams setup (issue #98 , issue #43 ) · ecaf51fa
  Valentina Galata authored 4 years ago
  
  ecaf51fa
Oct 12, 2020
- assembly: updated operams version (issue #98 ) · 6f4d0c12
  Valentina Galata authored 4 years ago
  
  6f4d0c12
Oct 08, 2020
- bug fix: operams installtion (issue #43 ) · 77f0442c
  Valentina Galata authored 4 years ago
  
  77f0442c
- fix: rm dependency check from operams installation cmd (issue #43 ) · d0566bba
  Valentina Galata authored 4 years ago
  
  d0566bba
- fixed a bug: wrong symbol in operams installation cmd (issue #43 ) · bc348a21
  Valentina Galata authored 4 years ago
  
  bc348a21
- fixed a bug: link for final fasta for flye · 059849c2
  Valentina Galata authored 4 years ago
  
  059849c2
- assembly: updated input (preproc files); operams update; not finished - polishing/filtering · 0706a827
  Valentina Galata authored 4 years ago
  
  0706a827
- updated operams installation rule and log file name for rgi db · d1cb5e4a
  Valentina Galata authored 4 years ago
  
  d1cb5e4a