Commits · 448d72a11e9b1d7c72502e56966efde9319a7ce6 · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Oct 13, 2020
- 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
Jun 30, 2020
- fixed a type in analysis.smk (rules/steps) in target paths · 37c82d2b
  Valentina Galata authored 4 years ago
  
  37c82d2b
- analysis step update: updated quast/bbmap/cdhit conda YAML; other minor updates · 7bc8732e
  Valentina Galata authored 4 years ago
  
  7bc8732e
Jun 26, 2020
- added conda YAML for mmseqs2 · 53e5cbd7
  Valentina Galata authored 4 years ago
  
  53e5cbd7
- new conda YAML for cd-hit · ef74e76a
  Valentina Galata authored 4 years ago
  
  ef74e76a
Jun 25, 2020
- major update: mapping, assembly, annotation, analysis (not all tested) · 332216ef
  Valentina Galata authored 4 years ago
  
  332216ef
Jun 14, 2020
- mv old rule and step files to backup sub-folder (will be replaced by new files) · 0872ae49
  Valentina Galata authored 4 years ago
  
  0872ae49
Jun 09, 2020
- mv rule files · 697cb518
  Valentina Galata authored 4 years ago
  
  697cb518
- made all non-script files not executable; scripts are only executable by user and group · c372fce1
  Valentina Galata authored 4 years ago
  
  c372fce1
- mv workflows/rules/scripts/env/config/src from 2019_GDB · d4e02299
  Valentina Galata authored 4 years ago
  
  d4e02299
Jun 03, 2020
- config/import clean-up · ac10becd
  Valentina Galata authored 4 years ago
  
  ac10becd
- config/import clean-up: analysis · c574d4e1
  Valentina Galata authored 4 years ago
  
  c574d4e1
- config/import clean-up: analysis · 1e8401ff
  Valentina Galata authored 4 years ago
  
  1e8401ff
- made FAA temp in rgi input rules; other minor changes (issue #29 ) · 2ab9da0b
  Valentina Galata authored 4 years ago
  
  2ab9da0b
- added rgi (issue #29 ) · 5a7350e8
  Valentina Galata authored 4 years ago
  
  5a7350e8
- added plasflow (issue #28 ): includes important updates of config and snakemake files · 32df69ba
  Valentina Galata authored 4 years ago
  
  32df69ba
May 30, 2020
- Update ANALYSIS_RULES · b40e3bfb
  Susheel Busi authored 4 years ago
  
  b40e3bfb
- removing the date flag from CASC shell due to errors · aeb752cd
  Susheel Busi authored 4 years ago
  
  aeb752cd
- fixed the path for the minced_CRISPR_output.txt file, and also fixed the CASC issue · e98663ed
  Susheel Busi authored 4 years ago
  
  e98663ed
- included calling the date in the shell · 43c3dfab
  Susheel Busi authored 4 years ago
  
  43c3dfab
- edited the ANALYSIS_RULES for running CASC · 88ef1d4d
  Susheel Busi authored 4 years ago
  
  88ef1d4d