Commits · 6338f3c1849be08b29328e7b31a79f7aea780ccd · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Jul 31, 2020
- Merge branch 'cleanup' · 6338f3c1
  Valentina Galata authored 4 years ago
  
  6338f3c1
- update of GIS20 config (changes made back then to re-run) · 0f2fd1e5
  Valentina Galata authored 4 years ago
  
  0f2fd1e5
- issue #73 : added barrnap conda yaml; report: barrnap figure · 24f2c2bc
  Valentina Galata authored 4 years ago
  
  24f2c2bc
- issue #73 : added barrnap rules · eaa1f261
  Valentina Galata authored 4 years ago
  
  eaa1f261
- issue #74 (config validation); updated GDB config · bc0803ca
  Valentina Galata authored 4 years ago
  
  bc0803ca
- analysis/report: mash on reads (issue #58 ); minor formatting changes · ce573af6
  Valentina Galata authored 4 years ago
  
  ce573af6
Jul 30, 2020
- report: added gene length distribution plots (issue #71 ) · 7cda6761
  Valentina Galata authored 4 years ago
  
  7cda6761
- report: diamond: query and subject coverage, other updates (issue #69 ) · 7f7d5f37
  Valentina Galata authored 4 years ago
  
  7f7d5f37
Jul 24, 2020
- cdhit: length diff cutoff (issue #68 ) · c84c44d1
  Valentina Galata authored 4 years ago
  
  c84c44d1
- added kaiju env (issue #67 ) · d8eca279
  Valentina Galata authored 4 years ago
  
  d8eca279
- updated GDB configs · a07275a8
  Valentina Galata authored 4 years ago
  
  a07275a8
- updated tax step: kaiju summary (issue #67 ) · d7fd67ec
  Valentina Galata authored 4 years ago
  
  d7fd67ec
- tax step: added kaiju (cdhit, issue #67 ), minor changes for kraken2 rules,... · 726b11a8
  Valentina Galata authored 4 years ago
  
  tax step: added kaiju (cdhit, issue #67), minor changes for kraken2 rules, updated Snakefile and GDB configs
  726b11a8
- updated init.smk and main Snakefile (tax is switched off) · f867b451
  Valentina Galata authored 4 years ago
  
  f867b451
- updated GDB slurm.config · 67b2a546
  Valentina Galata authored 4 years ago
  
  67b2a546
- renamed mash rules · b44dd29d
  Valentina Galata authored 4 years ago
  
  b44dd29d
- updated targets in mapping step (issue #66 ) · 44e79e5a
  Valentina Galata authored 4 years ago
  
  44e79e5a
- report update · d1e53f46
  Valentina Galata authored 4 years ago
  
  d1e53f46
Jul 23, 2020
- updated GDB contig files · cb0e17b2
  Valentina Galata authored 4 years ago
  
  cb0e17b2
- adjusted annotation step (issue #66 , not tested yet) · 4d60da61
  Valentina Galata authored 4 years ago
  
  4d60da61
- cleanup: replace out/err log by log; changed params for metaquast · 57bd9934
  Valentina Galata authored 4 years ago
  
  57bd9934
- cleanup: replace out/err log by log · 5fbb942a
  Valentina Galata authored 4 years ago
  
  5fbb942a
- added contig filtering (not adjusted yet) (issue #66 ) · 73b62b1d
  Valentina Galata authored 4 years ago
  
  73b62b1d
Jul 22, 2020
- report update (incl metat polished assemblies) (issue #52 ) · 680d8114
  Valentina Galata authored 4 years ago
  
  680d8114
- cleaned up GDB config · c20052fd
  Valentina Galata authored 4 years ago
  
  c20052fd
- updated GDB config files · 4ee61449
  Valentina Galata authored 4 years ago
  
  4ee61449
- assembly polishing w/ racon and metat (issue #52 ) · 7778266f
  Valentina Galata authored 4 years ago
  
  7778266f
Jul 20, 2020
- added notes (short scripts etc.) incl. scripts for issue #65 · ea06388a
  Valentina Galata authored 4 years ago
  
  ea06388a
- cleanup: rm backup files · 411efdef
  Valentina Galata authored 4 years ago
  
  411efdef
- report: added diamond density plot · 3bf391ef
  Valentina Galata authored 4 years ago
  
  3bf391ef
Jul 17, 2020
- added mash screen analysis (issue #64 ) · 04c4ddd4
  Valentina Galata authored 4 years ago
  
  04c4ddd4
- updated slurm.yaml for GIS20: longer runtime for mapping_assembly_uniq · e12bfc99
  Valentina Galata authored 4 years ago
  
  e12bfc99
Jul 16, 2020
- updated configs: updated mapping rule names in slurm configs; other minor changes · b97da7d9
  Valentina Galata authored 4 years ago
  
  b97da7d9
Jul 14, 2020
- updated configs for ganges dataset (issue #60 ) · 6a052006
  Valentina Galata authored 4 years ago
  
  6a052006
- forgot to rm mapping and coverage from assembly step · d6f1b932
  Valentina Galata authored 4 years ago
  
  d6f1b932
Jul 13, 2020
- updated ganges config files; fixed a bug in init.smk and basecalling.smk · 708d8bf5
  Valentina Galata authored 4 years ago
  
  708d8bf5
- updated ganges config.yaml (merged); changed how input files are linked · a538f7b8
  Valentina Galata authored 4 years ago
  
  a538f7b8
- changed how input files are linked · 91629224
  Valentina Galata authored 4 years ago
  
  91629224
- updated ganges config.yaml · 7d13fd2c
  Valentina Galata authored 4 years ago
  
  7d13fd2c
- config files etc for ganges sample · 92935da4
  Susheel Busi authored 4 years ago
  
  92935da4