Commits · 7c15b717d52e1032d5299b1cfbd823589cd20b8a · ESB / ONT_pilot_gitlab

Nov 05, 2020
- added header extraction rules to Snakefile · 7c15b717
  Susheel Busi authored 4 years ago
  
  7c15b717
- updated launcher file · f54e24e7
  Susheel Busi authored 4 years ago
  
  f54e24e7
- added rules for diamond analyses · 17bb9496
  Susheel Busi authored 4 years ago
  
  17bb9496
- updated rules for downloading and concatenating reference genomes · 802dba2d
  Susheel Busi authored 4 years ago
  
  802dba2d
- updated files for zymo reference genome analyses · bb1b92c3
  Susheel Busi authored 4 years ago
  
  bb1b92c3
Aug 21, 2020
- updated readme; configs: updated conda env path in all sbatch.sh files · cf5125be
  Valentina Galata authored 4 years ago
  
  cf5125be
- configs: sbatch.sh: run snakemake only if conda env activation has worked · 34ac0857
  Valentina Galata authored 4 years ago
  
  34ac0857
- Update sbatch.sh · 38268814
  Susheel Busi authored 4 years ago
  
  38268814
Aug 20, 2020
- Zymo/GSI20 configs: replaced main conda env path · 4ac143ff
  Valentina Galata authored 4 years ago
  
  4ac143ff
Aug 19, 2020
- GIS20/Zymo configs: fixed a typo · 6fa78459
  Valentina Galata authored 4 years ago
  
  6fa78459
- updated configs · db86679c
  Valentina Galata authored 4 years ago
  
  db86679c
- polishing update: changed polishing strategy, updated racon conda yaml to... · 1ffcfe82
  Valentina Galata authored 4 years ago
  
  polishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)
  1ffcfe82
Aug 18, 2020
- updated GDB config: added mapping back to the steps · e71b9507
  Valentina Galata authored 4 years ago
  
  e71b9507
Aug 17, 2020
- GIS20/Zymo config: sortmerna/bbmap update · 3df1c26a
  Valentina Galata authored 4 years ago
  
  3df1c26a
- GDB config: sortmerna/bbmap update · 7c16689b
  Valentina Galata authored 4 years ago
  
  7c16689b
- GDB config (slurm): rule mapping_bwa_mem_assembly_hyhy · e3eae03c
  Valentina Galata authored 4 years ago
  
  e3eae03c
- GIS20 configs: updated · 992a11c4
  Valentina Galata authored 4 years ago
  
  992a11c4
- zymo configs: updated · 14c69148
  Valentina Galata authored 4 years ago
  
  14c69148
Aug 16, 2020
- GDB config: sormerna update · 88debfb8
  Valentina Galata authored 4 years ago
  
  88debfb8
- GDB config: sormerna cores and runtime, other minor changes · 7bca601e
  Valentina Galata authored 4 years ago
  
  7bca601e
- GDB config: more cores and time for sortmerna · 3a42ed49
  Valentina Galata authored 4 years ago
  
  3a42ed49
Aug 14, 2020
- updated GDB config files · 48aa5933
  Valentina Galata authored 4 years ago
  
  48aa5933
Aug 13, 2020
- updated GDB config files · ae3b5884
  Valentina Galata authored 4 years ago
  
  ae3b5884
Aug 03, 2020
- updated GDB config files · 689e112b
  Valentina Galata authored 4 years ago
  
  689e112b
Jul 31, 2020
- update of GIS20 config (changes made back then to re-run) · 0f2fd1e5
  Valentina Galata authored 4 years ago
  
  0f2fd1e5
- issue #74 (config validation); updated GDB config · bc0803ca
  Valentina Galata authored 4 years ago
  
  bc0803ca
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
- cleaned up GDB config · c20052fd
  Valentina Galata authored 4 years ago
  
  c20052fd
- updated GDB config files · 4ee61449
  Valentina Galata authored 4 years ago
  
  4ee61449
Jul 17, 2020
- updated slurm.yaml for GIS20: longer runtime for mapping_assembly_uniq · e12bfc99
  Valentina Galata authored 4 years ago
  
  e12bfc99
Jul 16, 2020
- updated configs: updated mapping rule names in slurm configs; other minor changes · b97da7d9
  Valentina Galata authored 4 years ago
  
  b97da7d9
Jul 14, 2020
- updated configs for ganges dataset (issue #60 ) · 6a052006
  Valentina Galata authored 4 years ago
  
  6a052006
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