Commits · 88debfb87a7e01a62b109b74c6d04f63b3ebe27e · ESB / ONT_pilot_gitlab · GitLab

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Aug 16, 2020
- 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
- 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