Commits · 689e112bf859ec1248a080105c10385d0b01a724 · ESB / ONT_pilot_gitlab

Aug 03, 2020
- updated GDB config files · 689e112b
  Valentina Galata authored 4 years ago
  
  689e112b
Jul 24, 2020
- updated GDB configs · a07275a8
  Valentina Galata authored 4 years ago
  
  a07275a8
- tax step: added kaiju (cdhit, issue #67 ), minor changes for kraken2 rules,... · 726b11a8
  Valentina Galata authored 4 years ago
  
  tax step: added kaiju (cdhit, issue #67), minor changes for kraken2 rules, updated Snakefile and GDB configs
  726b11a8
- updated GDB slurm.config · 67b2a546
  Valentina Galata authored 4 years ago
  
  67b2a546
Jul 23, 2020
- updated GDB contig files · cb0e17b2
  Valentina Galata authored 4 years ago
  
  cb0e17b2
Jul 22, 2020
- updated GDB config files · 4ee61449
  Valentina Galata authored 4 years ago
  
  4ee61449
Jul 16, 2020
- updated configs: updated mapping rule names in slurm configs; other minor changes · b97da7d9
  Valentina Galata authored 4 years ago
  
  b97da7d9
Jul 13, 2020
- changed init: LR can have FASTQ (instead of FAST5); updated configs (issue... · e41852d5
  Valentina Galata authored 4 years ago
  
  changed init: LR can have FASTQ (instead of FAST5); updated configs (issue #56); other minor changes
  e41852d5
Jul 09, 2020
- added circ_contigs_fasta.py (issue #53 ); added kraken2 (tax) (issue #55 ) · 334acc25
  Valentina Galata authored 4 years ago
  
  334acc25
Jun 30, 2020
- added configs for GDB (same as the ones in config/); mv sbatch.sh to config/ (issue #45 ) · 7ccc3d89
  Valentina Galata authored 4 years ago
  
  7ccc3d89
Jun 26, 2020
- updated prodigal runtime in slurm.yaml · 2955bc7d
  Valentina Galata authored 4 years ago
  
  2955bc7d
- updated slurm.config: plasflow should run on bigmem · a9ce46ad
  Valentina Galata authored 4 years ago
  
  a9ce46ad
Jun 25, 2020
- config and slurm update · b5077eb7
  Valentina Galata authored 4 years ago
  
  b5077eb7
- major update: mapping, assembly, annotation, analysis (not all tested) · 332216ef
  Valentina Galata authored 4 years ago
  
  332216ef
- updated slurm config and changed a rule name · 23c610cc
  Valentina Galata authored 4 years ago
  
  23c610cc
Jun 14, 2020
- 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
- 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
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
- initial fast5 setup, basecalling and nanostat · 5feedaab
  Valentina Galata authored 4 years ago
  
  5feedaab