Commits · dddbbda52cb03f63a8273eb5e45dc8b5503454ff · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Jun 24, 2020
- updated gitignore · dddbbda5
  Valentina Galata authored 4 years ago
  
  dddbbda5
- updated annotation (not tested) · f83435a5
  Valentina Galata authored 4 years ago
  
  f83435a5
- changed structure to incl metat: updated prepare_input and preprocessing, other minor changes · a17cbe8b
  Valentina Galata authored 4 years ago
  
  a17cbe8b
- mv main snakemake file, rm sep. preproc files for sr/lr · d305f372
  Valentina Galata authored 4 years ago
  
  d305f372
Jun 14, 2020
- annotation step update (not finished): added RGI and PlasFlow · 2b926580
  Valentina Galata authored 4 years ago
  
  2b926580
- started to incl annotation (not finished) · c119ac8e
  Valentina Galata authored 4 years ago
  
  c119ac8e
- mv old rule and step files to backup sub-folder (will be replaced by new files) · 0872ae49
  Valentina Galata authored 4 years ago
  
  0872ae49
- increased num of cpus and running time for medaka · 585f85df
  Valentina Galata authored 4 years ago
  
  585f85df
Jun 13, 2020
- assembly step update: new file structure · 6c29af9a
  Valentina Galata authored 4 years ago
  
  6c29af9a
Jun 12, 2020
- rm workflow/steps/mapping.smk (incl in assembly) · cd08880e
  Valentina Galata authored 4 years ago
  
  cd08880e
- changed mapping, added polishing and (ave) cov · 3981a117
  Valentina Galata authored 4 years ago
  
  3981a117
- added mapping · d9fec571
  Valentina Galata authored 4 years ago
  
  d9fec571
- minor update in workflow/rules/assembly.smk · fa54a2e9
  Valentina Galata authored 4 years ago
  
  fa54a2e9
Jun 11, 2020
- bug fix in rules/preprocessing_lr.smk: output path in guppy CMD · 34e77253
  Valentina Galata authored 4 years ago
  
  34e77253
- updated cmd for megahit in rules/assembly.smk · f8c7ed5e
  Valentina Galata authored 4 years ago
  
  f8c7ed5e
- bug in rules/preprocessing_lr.smk: fixed guppy cmd · 124a63c0
  Valentina Galata authored 4 years ago
  
  124a63c0
- sbatch.sh: more cores for snakemake · ac1679b0
  Valentina Galata authored 4 years ago
  
  ac1679b0
Jun 10, 2020
- updated slurm.yaml · a9adb619
  Valentina Galata authored 4 years ago
  
  a9adb619
- init setup for preprocessing and assembly · 6cbf5ed6
  Valentina Galata authored 4 years ago
  
  6cbf5ed6
- updated input preparation rules · ab685564
  Valentina Galata authored 4 years ago
  
  ab685564
- initial fast5 setup, basecalling and nanostat · 5feedaab
  Valentina Galata authored 4 years ago
  
  5feedaab
- renamed config · 23ad860f
  Valentina Galata authored 4 years ago
  
  23ad860f
- rm remaining 2019_GDB · b03c1ea7
  Valentina Galata authored 4 years ago
  
  b03c1ea7
- rm checkm_files · e09fb17c
  Valentina Galata authored 4 years ago
  
  e09fb17c
Jun 09, 2020
- updated changes from commit a763ff07 and some other minor updates · ede047bc
  Valentina Galata authored 4 years ago
  
  ede047bc
- minor changes in Snakemake file · 2e17bac2
  Valentina Galata authored 4 years ago
  
  2e17bac2
- updated step analysis · 98955ae9
  Valentina Galata authored 4 years ago
  
  98955ae9
- updated step taxonomy · a020fdeb
  Valentina Galata authored 4 years ago
  
  a020fdeb
- updated step binning · c27407fb
  Valentina Galata authored 4 years ago
  
  c27407fb
- updated step mapping · da325067
  Valentina Galata authored 4 years ago
  
  da325067
- updated step metaT · 1ff81596
  Valentina Galata authored 4 years ago
  
  1ff81596
- updated step mmseq and Snakemake file · 1a3372a3
  Valentina Galata authored 4 years ago
  
  1a3372a3
- updated step assembly_annotation and checkpoint_assembly_annotation · 7ea13441
  Valentina Galata authored 4 years ago
  
  7ea13441
- updated step assembly_annotation · 4777cc38
  Valentina Galata authored 4 years ago
  
  4777cc38
- mv config out of workflow · d09a3470
  Valentina Galata authored 4 years ago
  
  d09a3470
- mv rule files · 697cb518
  Valentina Galata authored 4 years ago
  
  697cb518
- mv 2019_GDB/updated_SNAKEFILE -> Snakefile · 923c4b46
  Valentina Galata authored 4 years ago
  
  923c4b46
- made all non-script files not executable; scripts are only executable by user and group · c372fce1
  Valentina Galata authored 4 years ago
  
  c372fce1
- mv workflows/rules/scripts/env/config/src from 2019_GDB · d4e02299
  Valentina Galata authored 4 years ago
  
  d4e02299
- rm not relevant files and files to be replaced by 2019_GDB · 93bda1eb
  Valentina Galata authored 4 years ago
  
  93bda1eb