Commits · 708d8bf5030af6665860fd8773725938d97219e0 · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Jul 13, 2020
- updated ganges config files; fixed a bug in init.smk and basecalling.smk · 708d8bf5
  Valentina Galata authored 4 years ago
  
  708d8bf5
- updated ganges config.yaml · 7d13fd2c
  Valentina Galata authored 4 years ago
  
  7d13fd2c
- config files etc for ganges sample · 92935da4
  Susheel Busi authored 4 years ago
  
  92935da4
- added configs for GIS20 (issue #57 ) · ee9d2237
  Valentina Galata authored 4 years ago
  
  ee9d2237
- minor changes in sbatch.sh (GDB, Zymo) · 6809a185
  Valentina Galata authored 4 years ago
  
  6809a185
- renamed in config/: Zymo-GridION-EVEN-BB-SN to Zymo · 8d46c000
  Valentina Galata authored 4 years ago
  
  8d46c000
- 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
- updated config.yaml for GDB and mock · b5ad0b08
  Valentina Galata authored 4 years ago
  
  b5ad0b08
Jul 09, 2020
- added mash analysis (issue #58 ) · e08b0f30
  Valentina Galata authored 4 years ago
  
  e08b0f30
- added circ_contigs_fasta.py (issue #53 ); added kraken2 (tax) (issue #55 ) · 334acc25
  Valentina Galata authored 4 years ago
  
  334acc25
- updated Zymo-GridION-EVEN-BB-SN/sbatch.sh · abc1d13b
  Valentina Galata authored 4 years ago
  
  abc1d13b
- mv config/sbatch.sh to sub-folder Zymo-GridION-EVEN-BB-SN · 931d24db
  Valentina Galata authored 4 years ago
  
  931d24db
- updated slurm file for MOCK run · 6ccd4acc
  Susheel Busi authored 4 years ago
  
  6ccd4acc
- updated sbatch file for MOCK run · f6f57407
  Susheel Busi authored 4 years ago
  
  f6f57407
Jul 08, 2020
- updated sbatch.sh for GDB · 2362a407
  Valentina Galata authored 4 years ago
  
  2362a407
- added slurm.yaml for Zymo-GridION-EVEN-BB-SN; rm not used configs · c6afa55b
  Valentina Galata authored 4 years ago
  
  c6afa55b
Jul 07, 2020
- slurm.yaml file updated for Zymo-MOCK-EVEN sample increasing time limit for bwa_mem_assembly · 82fd036f
  Susheel Busi authored 4 years ago
  
  82fd036f
Jul 01, 2020
- adding the config.yaml for the Zymo EVEN mock run · f5671a0f
  Susheel Busi authored 4 years ago
  
  f5671a0f
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
- added workflow to create multi-fast5 files; added configs for Zymo-GridION-EVEN-BB-SN (issue #45 ) · afd8885b
  Valentina Galata authored 4 years ago
  
  afd8885b
- analysis step update: updated quast/bbmap/cdhit conda YAML; other minor updates · 7bc8732e
  Valentina Galata authored 4 years ago
  
  7bc8732e
Jun 26, 2020
- rm CHANGELOG and not used config · 941b430d
  Valentina Galata authored 4 years ago
  
  941b430d
- updated prodigal runtime in slurm.yaml · 2955bc7d
  Valentina Galata authored 4 years ago
  
  2955bc7d
- minor updates in config.yaml · 9ab20570
  Valentina Galata authored 4 years ago
  
  9ab20570
- updated slurm.config: plasflow should run on bigmem · a9ce46ad
  Valentina Galata authored 4 years ago
  
  a9ce46ad
- new rules to setup tools/data; added casc installation (issue #41 ) · 2ac06d02
  Valentina Galata authored 4 years ago
  
  2ac06d02
Jun 25, 2020
- config and slurm update · b5077eb7
  Valentina Galata authored 4 years ago
  
  b5077eb7
- mv figures.yml to config/ · 89ac6906
  Valentina Galata authored 4 years ago
  
  89ac6906
- 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 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
- changed structure to incl metat: updated prepare_input and preprocessing, other minor changes · a17cbe8b
  Valentina Galata authored 4 years ago
  
  a17cbe8b
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