Commits · fe910ac4e1816ba7ef4a4921ceb76f1445ee1735 · ESB / ONT_pilot_gitlab

13 Aug, 2020 4 commits
- updated assembler names and colors in workflow_report/scripts/utils.R · fe910ac4
  Valentina Galata authored Aug 13, 2020
  
  fe910ac4
- updated GDB config files · ae3b5884
  Valentina Galata authored Aug 13, 2020
  
  ae3b5884
- updated config schema · 6690266a
  Valentina Galata authored Aug 13, 2020
  
  6690266a
- added lr assembler canu (issue #72 ) · d26b438f
  Valentina Galata authored Aug 13, 2020
  
  d26b438f
10 Aug, 2020 2 commits
- scripts: add annot to diamond hits and find gene clusters (issue #70): will be... · 14d7afdf
  Valentina Galata authored Aug 10, 2020
```
scripts: add annot to diamond hits and find gene clusters (issue #70): will be included later in the pipeline
```
  14d7afdf
- added threads to diamond view command in annotation.smk · 66acc49c
  Valentina Galata authored Aug 10, 2020
  
  66acc49c
03 Aug, 2020 2 commits
- updated GDB config files · 689e112b
  Valentina Galata authored Aug 03, 2020
  
  689e112b
- issue #72 : added wtdbg2 (LR assembler) · b6dfa4c7
  Valentina Galata authored Aug 03, 2020
  
  b6dfa4c7
31 Jul, 2020 7 commits
- cleanup after merging · 2b965a5d
  Valentina Galata authored Jul 31, 2020
  
  2b965a5d
- Merge branch 'cleanup' · 6338f3c1
  Valentina Galata authored Jul 31, 2020
  
  6338f3c1
- update of GIS20 config (changes made back then to re-run) · 0f2fd1e5
  Valentina Galata authored Jul 31, 2020
  
  0f2fd1e5
- issue #73 : added barrnap conda yaml; report: barrnap figure · 24f2c2bc
  Valentina Galata authored Jul 31, 2020
  
  24f2c2bc
- issue #73 : added barrnap rules · eaa1f261
  Valentina Galata authored Jul 31, 2020
  
  eaa1f261
- issue #74 (config validation); updated GDB config · bc0803ca
  Valentina Galata authored Jul 31, 2020
  
  bc0803ca
- analysis/report: mash on reads (issue #58 ); minor formatting changes · ce573af6
  Valentina Galata authored Jul 31, 2020
  
  ce573af6
30 Jul, 2020 2 commits
- report: added gene length distribution plots (issue #71 ) · 7cda6761
  Valentina Galata authored Jul 30, 2020
  
  7cda6761
- report: diamond: query and subject coverage, other updates (issue #69 ) · 7f7d5f37
  Valentina Galata authored Jul 30, 2020
  
  7f7d5f37
24 Jul, 2020 10 commits
- cdhit: length diff cutoff (issue #68 ) · c84c44d1
  Valentina Galata authored Jul 24, 2020
  
  c84c44d1
- added kaiju env (issue #67 ) · d8eca279
  Valentina Galata authored Jul 24, 2020
  
  d8eca279
- updated GDB configs · a07275a8
  Valentina Galata authored Jul 24, 2020
  
  a07275a8
- updated tax step: kaiju summary (issue #67 ) · d7fd67ec
  Valentina Galata authored Jul 24, 2020
  
  d7fd67ec
- tax step: added kaiju (cdhit, issue #67), minor changes for kraken2 rules,... · 726b11a8
  Valentina Galata authored Jul 24, 2020
```
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 Jul 24, 2020
  
  f867b451
- updated GDB slurm.config · 67b2a546
  Valentina Galata authored Jul 24, 2020
  
  67b2a546
- renamed mash rules · b44dd29d
  Valentina Galata authored Jul 24, 2020
  
  b44dd29d
- updated targets in mapping step (issue #66 ) · 44e79e5a
  Valentina Galata authored Jul 24, 2020
  
  44e79e5a
- report update · d1e53f46
  Valentina Galata authored Jul 24, 2020
  
  d1e53f46
23 Jul, 2020 5 commits
- updated GDB contig files · cb0e17b2
  Valentina Galata authored Jul 23, 2020
  
  cb0e17b2
- adjusted annotation step (issue #66 , not tested yet) · 4d60da61
  Valentina Galata authored Jul 23, 2020
  
  4d60da61
- cleanup: replace out/err log by log; changed params for metaquast · 57bd9934
  Valentina Galata authored Jul 23, 2020
  
  57bd9934
- cleanup: replace out/err log by log · 5fbb942a
  Valentina Galata authored Jul 23, 2020
  
  5fbb942a
- added contig filtering (not adjusted yet) (issue #66 ) · 73b62b1d
  Valentina Galata authored Jul 23, 2020
  
  73b62b1d
22 Jul, 2020 4 commits
- report update (incl metat polished assemblies) (issue #52 ) · 680d8114
  Valentina Galata authored Jul 22, 2020
  
  680d8114
- cleaned up GDB config · c20052fd
  Valentina Galata authored Jul 22, 2020
  
  c20052fd
- updated GDB config files · 4ee61449
  Valentina Galata authored Jul 22, 2020
  
  4ee61449
- assembly polishing w/ racon and metat (issue #52 ) · 7778266f
  Valentina Galata authored Jul 22, 2020
  
  7778266f
20 Jul, 2020 3 commits
- added notes (short scripts etc.) incl. scripts for issue #65 · ea06388a
  Valentina Galata authored Jul 20, 2020
  
  ea06388a
- cleanup: rm backup files · 411efdef
  Valentina Galata authored Jul 20, 2020
  
  411efdef
- report: added diamond density plot · 3bf391ef
  Valentina Galata authored Jul 20, 2020
  
  3bf391ef
17 Jul, 2020 1 commit
- added mash screen analysis (issue #64 ) · 04c4ddd4
  Valentina Galata authored Jul 17, 2020
  
  04c4ddd4