Commits · 6f4d0c12dd320fe8bb2e4e25979e5b948b9e3599 · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Oct 12, 2020
- assembly: updated operams version (issue #98 ) · 6f4d0c12
  Valentina Galata authored 4 years ago
  
  6f4d0c12
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
- operamse: checked out release v0.8.3 (latest) (issue #43 ) · fe85a8a6
  Valentina Galata authored 4 years ago
  
  fe85a8a6
- 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
- added operams as a git submodule (issue #43 ) · a5ccd137
  Valentina Galata authored 4 years ago
  
  a5ccd137
- 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
- updated GDB config files (issue #54 ) · 3370f1b8
  Valentina Galata authored 4 years ago
  
  3370f1b8
- 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 22, 2020
- notes: script for segmentation analysis of contig cov (issue #84 ) · c2d4784c
  Valentina Galata authored 4 years ago
  
  c2d4784c
Sep 16, 2020
- report: updated plots (mostly themes) · c48ede7b
  Valentina Galata authored 4 years ago
  
  c48ede7b
Sep 15, 2020
- notes: plots and multimodality test for contig cov (issye #84 ) · b7870822
  Valentina Galata authored 4 years ago
  
  b7870822
- report: added shapes to cdhit scatter plot · d9e49f81
  Valentina Galata authored 4 years ago
  
  d9e49f81
Sep 14, 2020
- report: changed zoom in gene length plot · 53aba75b
  Valentina Galata authored 4 years ago
  
  53aba75b
- report: updated cdhit plots (issue #84 ) · 6a0c99c5
  Valentina Galata authored 4 years ago
  
  6a0c99c5
- report: minor change in report.R (axis titles in gene len fig) · b380f34c
  Valentina Galata authored 4 years ago
  
  b380f34c
- report: new cdhit summary and plots (issue #84 ); other minor changes · 9e197abd
  Valentina Galata authored 4 years ago
  
  9e197abd
- report: rm pack version from r.yaml (prev env version cannot be recreated) · aa32eadf
  Valentina Galata authored 4 years ago
  
  aa32eadf
- 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
Sep 10, 2020
- issue #77 : cov plot example - updated · 1600fdd4
  Valentina Galata authored 4 years ago
  
  1600fdd4
- issue #77 : cov plot example · 1257fcdb
  Valentina Galata authored 4 years ago
  
  1257fcdb
Sep 09, 2020
- Merge branch 'master' of ssh://git-r3lab-server.uni.lu:8022/susheel.busi/ont_pilot_gitlab · 66bfe0c3
  Valentina Galata authored 4 years ago
  
  66bfe0c3
- issue #77 : notes to collected and plot stats for specialtigs (cdhit results) · f49767ce
  Valentina Galata authored 4 years ago
  
  f49767ce
Aug 28, 2020
- Update Snakefile · 45fe154c
  Susheel Busi authored 4 years ago
  
  45fe154c
Aug 21, 2020
- report: minor updates for the plots · b783d5d6
  Valentina Galata authored 4 years ago
  
  b783d5d6
- report: fixed a bug in rule collecting cdhit results · b8aec505
  Valentina Galata authored 4 years ago
  
  b8aec505
- updated readme; configs: updated conda env path in all sbatch.sh files · cf5125be
  Valentina Galata authored 4 years ago
  
  cf5125be
- report: updated names/colors of assemblers in utils.R · d6aef8eb
  Valentina Galata authored 4 years ago
  
  d6aef8eb