Commits · e71b9507efb44a0e34b762ccd1602003bdb34bb5 · ESB / ONT_pilot_gitlab · GitLab

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Aug 18, 2020
- updated GDB config: added mapping back to the steps · e71b9507
  Valentina Galata authored 4 years ago
  
  e71b9507
- report: update to include new assemblers; fixed tool order in cdhit/diamond plots · f45459a1
  Valentina Galata authored 4 years ago
  
  f45459a1
- mash: rm contig-screen analysis, fixed a bug (not all assemblies included in assembly sketch) · 9df850a2
  Valentina Galata authored 4 years ago
  
  9df850a2
- bbmap/bbduk to rm rrna reads: fixed cmd (issue #49 ) · ffdcc3aa
  Valentina Galata authored 4 years ago
  
  ffdcc3aa
Aug 17, 2020
- fixed paths for some mash rules (issue #79 ) · 31a6605d
  Valentina Galata authored 4 years ago
  
  31a6605d
- GIS20/Zymo config: sortmerna/bbmap update · 3df1c26a
  Valentina Galata authored 4 years ago
  
  3df1c26a
- GDB config: sortmerna/bbmap update · 7c16689b
  Valentina Galata authored 4 years ago
  
  7c16689b
- rm rrna reads: replaced sortmerna by bbmap (not tested) (issue #49 ) · 7fc7f4d1
  Valentina Galata authored 4 years ago
  
  7fc7f4d1
- GDB config (slurm): rule mapping_bwa_mem_assembly_hyhy · e3eae03c
  Valentina Galata authored 4 years ago
  
  e3eae03c
- GIS20 configs: updated · 992a11c4
  Valentina Galata authored 4 years ago
  
  992a11c4
- zymo configs: updated · 14c69148
  Valentina Galata authored 4 years ago
  
  14c69148
- changes need to include imp3 assembly (issue #76 ) · 29822190
  Valentina Galata authored 4 years ago
  
  29822190
- cdhit: changed renaming rule (issue #75 ), use '-s2 0.5' (issue #68 ) · 214f07ad
  Valentina Galata authored 4 years ago
  
  214f07ad
Aug 16, 2020
- notes: mmseqs2 example call · ae21c8ce
  Valentina Galata authored 4 years ago
  
  ae21c8ce
- GDB config: sormerna update · 88debfb8
  Valentina Galata authored 4 years ago
  
  88debfb8
- preproc step: sortmerna targets only if metat · b64323e5
  Valentina Galata authored 4 years ago
  
  b64323e5
- mapping step: fixed a bug - wrong names for targets · 64fe2ff8
  Valentina Galata authored 4 years ago
  
  64fe2ff8
- updated tax rules: kaiju for all proteins, kraken2 for filtered contigs only · e4c8ebf0
  Valentina Galata authored 4 years ago
  
  e4c8ebf0
- GDB config: sormerna cores and runtime, other minor changes · 7bca601e
  Valentina Galata authored 4 years ago
  
  7bca601e
- GDB config: more cores and time for sortmerna · 3a42ed49
  Valentina Galata authored 4 years ago
  
  3a42ed49
Aug 14, 2020
- notes: diamond hits scripts, mmseqs2 script (cdhit alternative) · 5a30755a
  Valentina Galata authored 4 years ago
  
  5a30755a
- updated GDB config files · 48aa5933
  Valentina Galata authored 4 years ago
  
  48aa5933
- added canu conda yaml (issue #72 ) · 9fba72e5
  Valentina Galata authored 4 years ago
  
  9fba72e5
- added sortmerna: preproc rule, mapping rule for sr split into metag/metat... · 3cc031ec
  Valentina Galata authored 4 years ago
  
  added sortmerna: preproc rule, mapping rule for sr split into metag/metat (issue #49); mapping rule for hyhy assembly (issue #76)
  3cc031ec
Aug 13, 2020
- updated assembler names and colors in workflow_report/scripts/utils.R · fe910ac4
  Valentina Galata authored 4 years ago
  
  fe910ac4
- updated GDB config files · ae3b5884
  Valentina Galata authored 4 years ago
  
  ae3b5884
- updated config schema · 6690266a
  Valentina Galata authored 4 years ago
  
  6690266a
- added lr assembler canu (issue #72 ) · d26b438f
  Valentina Galata authored 4 years ago
  
  d26b438f
Aug 10, 2020
- scripts: add annot to diamond hits and find gene clusters (issue #70 ): will be... · 14d7afdf
  Valentina Galata authored 4 years ago
  
  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 4 years ago
  
  66acc49c
Aug 03, 2020
- updated GDB config files · 689e112b
  Valentina Galata authored 4 years ago
  
  689e112b
- issue #72 : added wtdbg2 (LR assembler) · b6dfa4c7
  Valentina Galata authored 4 years ago
  
  b6dfa4c7
Jul 31, 2020
- cleanup after merging · 2b965a5d
  Valentina Galata authored 4 years ago
  
  2b965a5d
- 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