Commits · 2d314da5a326d5e7d20600f42f266b1768fc094e · ESB / ONT_pilot_gitlab · GitLab

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Jun 25, 2020
- report: minor update · 2d314da5
  Valentina Galata authored 4 years ago
  
  2d314da5
- updared diamond env (old one could not be build) · 12366758
  Valentina Galata authored 4 years ago
  
  12366758
- updared rgi env (old one could not be build) · 99f85045
  Valentina Galata authored 4 years ago
  
  99f85045
- report: initial setup · 46662031
  Valentina Galata authored 4 years ago
  
  46662031
- config and slurm update · b5077eb7
  Valentina Galata authored 4 years ago
  
  b5077eb7
- mv r.yml in report/ · a2b4e48f
  Valentina Galata authored 4 years ago
  
  a2b4e48f
- report: incl rmarkdown in r.yaml · 7908eb43
  Valentina Galata authored 4 years ago
  
  7908eb43
- mv figures.yml to config/ · 89ac6906
  Valentina Galata authored 4 years ago
  
  89ac6906
- rm data and src_SBB in report/ · 144b83c8
  Valentina Galata authored 4 years ago
  
  144b83c8
- rm src/; renamed snakemake file in report/ · e004fdf2
  Valentina Galata authored 4 years ago
  
  e004fdf2
- mv figures to report · e6aaae5f
  Valentina Galata authored 4 years ago
  
  e6aaae5f
- mv figures/src · 5c2713cc
  Valentina Galata authored 4 years ago
  
  5c2713cc
- major update: mapping, assembly, annotation, analysis (not all tested) · 332216ef
  Valentina Galata authored 4 years ago
  
  332216ef
- updated annotation rules (not tested) · 9dc7661e
  Valentina Galata authored 4 years ago
  
  9dc7661e
- updated slurm config and changed a rule name · 23c610cc
  Valentina Galata authored 4 years ago
  
  23c610cc
- assembly w/ operams: added perl for execution (issue #40 ), minor change of rule name · d8f4e72b
  Valentina Galata authored 4 years ago
  
  d8f4e72b
Jun 24, 2020
- assembly/mapping step: some fixes; added operams (issue #40 ) · e2acad95
  Valentina Galata authored 4 years ago
  
  e2acad95
- updated assembly/mapping step · aaacd0d1
  Valentina Galata authored 4 years ago
  
  aaacd0d1
- 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