Commits · 448d72a11e9b1d7c72502e56966efde9319a7ce6 · ESB / ONT_pilot_gitlab · GitLab

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Oct 13, 2020
- analysis: added fastani (issue #80 ) · 448d72a1
  Valentina Galata authored 4 years ago
  
  448d72a1
- analysis: added mashmap (issue #95 ) · 9d4e2111
  Valentina Galata authored 4 years ago
  
  9d4e2111
- analysis: quast: minor changes · cb87b5d7
  Valentina Galata authored 4 years ago
  
  cb87b5d7
- analysis: cdhit: simplified code, udpated params (issue #68 ) · 1002a9e8
  Valentina Galata authored 4 years ago
  
  1002a9e8
- analysis: simplified code for mash · dee459c6
  Valentina Galata authored 4 years ago
  
  dee459c6
- analysis: rm unused code for mmseqs2 · b6a340c1
  Valentina Galata authored 4 years ago
  
  b6a340c1
- analysis: rm code for circ contigs · f2edcfbf
  Valentina Galata authored 4 years ago
  
  f2edcfbf
- setup: updated operams setup (issue #98 , issue #43 ) · ecaf51fa
  Valentina Galata authored 4 years ago
  
  ecaf51fa
Oct 08, 2020
- bug fix: operams installtion (issue #43 ) · 77f0442c
  Valentina Galata authored 4 years ago
  
  77f0442c
- fix: rm dependency check from operams installation cmd (issue #43 ) · d0566bba
  Valentina Galata authored 4 years ago
  
  d0566bba
- fixed a bug: wrong symbol in operams installation cmd (issue #43 ) · bc348a21
  Valentina Galata authored 4 years ago
  
  bc348a21
- fixed a bug: link for final fasta for flye · 059849c2
  Valentina Galata authored 4 years ago
  
  059849c2
- assembly: updated input (preproc files); operams update; not finished - polishing/filtering · 0706a827
  Valentina Galata authored 4 years ago
  
  0706a827
- updated operams installation rule and log file name for rgi db · d1cb5e4a
  Valentina Galata authored 4 years ago
  
  d1cb5e4a
- minor: renamed two rules in workflow/rules/preprocessing.smk · 1c731cdc
  Valentina Galata authored 4 years ago
  
  1c731cdc
- envs: simplified and updated assembler yaml files · e79ffb6b
  Valentina Galata authored 4 years ago
  
  e79ffb6b
Oct 07, 2020
- setup rules: minor changes; operams setup (issue #43 ) · edb020ee
  Valentina Galata authored 4 years ago
  
  edb020ee
- envs: added operams yaml · 03fdf14e
  Valentina Galata authored 4 years ago
  
  03fdf14e
- preprocessing: links to final files · bb334cea
  Valentina Galata authored 4 years ago
  
  bb334cea
- envs: simplified yaml for bbmap/fastqc/nanostat · 464a2b02
  Valentina Galata authored 4 years ago
  
  464a2b02
- new conda YAML for flye (issue #90 ) · bb732b00
  Valentina Galata authored 4 years ago
  
  bb732b00
- 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