Commits · 3abb643ade60031f0cf270e9cdfaa894ea51aec3 · ESB / ONT_pilot_gitlab · GitLab

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Oct 07, 2020
- host contamination filtering w/ bbmap/bbtools (issue #54 ); other minor changes · 3abb643a
  Valentina Galata authored 4 years ago
  
  3abb643a
Sep 29, 2020
- added comment to diamond rule · d35ad664
  Valentina Galata authored 4 years ago
  
  d35ad664
Sep 14, 2020
- mapping/coverage: added utils/rule for ave gene/protein cov (issue #84 ) · 489c361b
  Valentina Galata authored 4 years ago
  
  489c361b
Sep 11, 2020
- mapping: changed genomecove_bg to per base coverage (issue #84 ) · e3af652b
  Valentina Galata authored 4 years ago
  
  e3af652b
- mapping: minor change in targets (ave cov for filtered contigs); new rule/targets (issue #84 ) · 7576bd59
  Valentina Galata authored 4 years ago
  
  7576bd59
Aug 19, 2020
- polishing update: changed polishing strategy, updated racon conda yaml to... · 1ffcfe82
  Valentina Galata authored 4 years ago
  
  polishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)
  1ffcfe82
Aug 18, 2020
- better expression to list targets for assembly step · fef9a05c
  Valentina Galata authored 4 years ago
  
  fef9a05c
- 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
- rm rrna reads: replaced sortmerna by bbmap (not tested) (issue #49 ) · 7fc7f4d1
  Valentina Galata authored 4 years ago
  
  7fc7f4d1
- 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
- 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
Aug 14, 2020
- notes: diamond hits scripts, mmseqs2 script (cdhit alternative) · 5a30755a
  Valentina Galata authored 4 years ago
  
  5a30755a
- 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
- 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
- issue #72 : added wtdbg2 (LR assembler) · b6dfa4c7
  Valentina Galata authored 4 years ago
  
  b6dfa4c7
Jul 31, 2020
- 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: 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 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
- 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
Jul 23, 2020
- 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
- assembly polishing w/ racon and metat (issue #52 ) · 7778266f
  Valentina Galata authored 4 years ago
  
  7778266f