Commits · e6aaae5f5b6f3fe21c4c00e47f01eb8c8a7fb93a · ESB / ONT_pilot_gitlab · GitLab

25 Jun, 2020 6 commits
- mv figures to report · e6aaae5f
  Valentina Galata authored Jun 25, 2020
  
  e6aaae5f
- mv figures/src · 5c2713cc
  Valentina Galata authored Jun 25, 2020
  
  5c2713cc
- major update: mapping, assembly, annotation, analysis (not all tested) · 332216ef
  Valentina Galata authored Jun 25, 2020
  
  332216ef
- updated annotation rules (not tested) · 9dc7661e
  Valentina Galata authored Jun 25, 2020
  
  9dc7661e
- updated slurm config and changed a rule name · 23c610cc
  Valentina Galata authored Jun 25, 2020
  
  23c610cc
- assembly w/ operams: added perl for execution (issue #40 ), minor change of rule name · d8f4e72b
  Valentina Galata authored Jun 25, 2020
  
  d8f4e72b
24 Jun, 2020 6 commits
- assembly/mapping step: some fixes; added operams (issue #40 ) · e2acad95
  Valentina Galata authored Jun 24, 2020
  
  e2acad95
- updated assembly/mapping step · aaacd0d1
  Valentina Galata authored Jun 24, 2020
  
  aaacd0d1
- updated gitignore · dddbbda5
  Valentina Galata authored Jun 24, 2020
  
  dddbbda5
- updated annotation (not tested) · f83435a5
  Valentina Galata authored Jun 24, 2020
  
  f83435a5
- changed structure to incl metat: updated prepare_input and preprocessing, other minor changes · a17cbe8b
  Valentina Galata authored Jun 24, 2020
  
  a17cbe8b
- mv main snakemake file, rm sep. preproc files for sr/lr · d305f372
  Valentina Galata authored Jun 24, 2020
  
  d305f372
14 Jun, 2020 4 commits
- annotation step update (not finished): added RGI and PlasFlow · 2b926580
  Valentina Galata authored Jun 14, 2020
  
  2b926580
- started to incl annotation (not finished) · c119ac8e
  Valentina Galata authored Jun 14, 2020
  
  c119ac8e
- mv old rule and step files to backup sub-folder (will be replaced by new files) · 0872ae49
  Valentina Galata authored Jun 14, 2020
  
  0872ae49
- increased num of cpus and running time for medaka · 585f85df
  Valentina Galata authored Jun 14, 2020
  
  585f85df
13 Jun, 2020 1 commit
- assembly step update: new file structure · 6c29af9a
  Valentina Galata authored Jun 13, 2020
  
  6c29af9a
12 Jun, 2020 4 commits
- rm workflow/steps/mapping.smk (incl in assembly) · cd08880e
  Valentina Galata authored Jun 12, 2020
  
  cd08880e
- changed mapping, added polishing and (ave) cov · 3981a117
  Valentina Galata authored Jun 12, 2020
  
  3981a117
- added mapping · d9fec571
  Valentina Galata authored Jun 12, 2020
  
  d9fec571
- minor update in workflow/rules/assembly.smk · fa54a2e9
  Valentina Galata authored Jun 12, 2020
  
  fa54a2e9
11 Jun, 2020 4 commits
- bug fix in rules/preprocessing_lr.smk: output path in guppy CMD · 34e77253
  Valentina Galata authored Jun 11, 2020
  
  34e77253
- updated cmd for megahit in rules/assembly.smk · f8c7ed5e
  Valentina Galata authored Jun 11, 2020
  
  f8c7ed5e
- bug in rules/preprocessing_lr.smk: fixed guppy cmd · 124a63c0
  Valentina Galata authored Jun 11, 2020
  
  124a63c0
- sbatch.sh: more cores for snakemake · ac1679b0
  Valentina Galata authored Jun 11, 2020
  
  ac1679b0
10 Jun, 2020 7 commits
- updated slurm.yaml · a9adb619
  Valentina Galata authored Jun 10, 2020
  
  a9adb619
- init setup for preprocessing and assembly · 6cbf5ed6
  Valentina Galata authored Jun 10, 2020
  
  6cbf5ed6
- updated input preparation rules · ab685564
  Valentina Galata authored Jun 10, 2020
  
  ab685564
- initial fast5 setup, basecalling and nanostat · 5feedaab
  Valentina Galata authored Jun 10, 2020
  
  5feedaab
- renamed config · 23ad860f
  Valentina Galata authored Jun 10, 2020
  
  23ad860f
- rm remaining 2019_GDB · b03c1ea7
  Valentina Galata authored Jun 10, 2020
  
  b03c1ea7
- rm checkm_files · e09fb17c
  Valentina Galata authored Jun 10, 2020
  
  e09fb17c
09 Jun, 2020 8 commits
- updated changes from commit a763ff07 and some other minor updates · ede047bc
  Valentina Galata authored Jun 09, 2020
  
  ede047bc
- minor changes in Snakemake file · 2e17bac2
  Valentina Galata authored Jun 09, 2020
  
  2e17bac2
- updated step analysis · 98955ae9
  Valentina Galata authored Jun 09, 2020
  
  98955ae9
- updated step taxonomy · a020fdeb
  Valentina Galata authored Jun 09, 2020
  
  a020fdeb
- updated step binning · c27407fb
  Valentina Galata authored Jun 09, 2020
  
  c27407fb
- updated step mapping · da325067
  Valentina Galata authored Jun 09, 2020
  
  da325067
- updated step metaT · 1ff81596
  Valentina Galata authored Jun 09, 2020
  
  1ff81596
- updated step mmseq and Snakemake file · 1a3372a3
  Valentina Galata authored Jun 09, 2020
  
  1a3372a3