Commits · 95f70fe7a1ba9eacb086560f075d8db2a561a0ee · ESB / ONT_pilot_gitlab · GitLab

Snippets Groups Projects

Jul 02, 2020
- workflow: rm partial gene counts rule from analysis (issue #50 ) · 95f70fe7
  Valentina Galata authored 4 years ago
  
  95f70fe7
- report: update for diamond/prodigal figures · d935fc15
  Valentina Galata authored 4 years ago
  
  d935fc15
- report: added total/partial gene counts (prodigal) (issue #50 ) · 347a86b8
  Valentina Galata authored 4 years ago
  
  347a86b8
- report: diamond query/subject length ratio (issue #22 ) · d876006c
  Valentina Galata authored 4 years ago
  
  d876006c
- report: added pct values to mappability barplots (issue #23 ) · 62dc23c4
  Valentina Galata authored 4 years ago
  
  62dc23c4
- changed contig length for idxstats report · d083e644
  Valentina Galata authored 4 years ago
  
  d083e644
- bug fix for casc (issue #48 ) · ac0fb73d
  Valentina Galata authored 4 years ago
  
  ac0fb73d
Jul 01, 2020
- report: added mappability (issue #23 and #27 ) · 19388d73
  Valentina Galata authored 4 years ago
  
  19388d73
- report: added mappability (flagstat) (issue #27 , issue #23 ) · 75c540bc
  Valentina Galata authored 4 years ago
  
  75c540bc
- analysis: quast: TSV instead of TXT as target (issue #46 ) · 1fdd1f1e
  Valentina Galata authored 4 years ago
  
  1fdd1f1e
- report: added crispr (issue #27 ) · 856b1e56
  Valentina Galata authored 4 years ago
  
  856b1e56
- updated utils.py · cea52b51
  Valentina Galata authored 4 years ago
  
  cea52b51
- mapping step: no metat output if no metat data given · 70895a6d
  Valentina Galata authored 4 years ago
  
  70895a6d
Jun 30, 2020
- renamed report/ into workflow_report/ · 07f363a3
  Valentina Galata authored 4 years ago
  
  07f363a3
- cleaned up report Snakefile · 9bc1f4e1
  Valentina Galata authored 4 years ago
  
  9bc1f4e1
- added rgi to the report (issue #27 ) · 3838040f
  Valentina Galata authored 4 years ago
  
  3838040f
- link to main conda YAML · 624e0671
  Valentina Galata authored 4 years ago
  
  624e0671
- 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
- added quast and plasflow to report (issue #27 ) · f6e245e7
  Valentina Galata authored 4 years ago
  
  f6e245e7
- fixed a type in analysis.smk (rules/steps) in target paths · 37c82d2b
  Valentina Galata authored 4 years ago
  
  37c82d2b
- analysis step update: updated quast/bbmap/cdhit conda YAML; other minor updates · 7bc8732e
  Valentina Galata authored 4 years ago
  
  7bc8732e
Jun 29, 2020
- sbatch.sh -- more cores for the pipeline · 3a97208b
  Valentina Galata authored 4 years ago
  
  3a97208b
- minor fix of regi setup rule · e403f026
  Valentina Galata authored 4 years ago
  
  e403f026
Jun 26, 2020
- rm CHANGELOG and not used config · 941b430d
  Valentina Galata authored 4 years ago
  
  941b430d
- updated/added messages to rules; rgi db is loaded in sep. rule · 10e83e92
  Valentina Galata authored 4 years ago
  
  10e83e92
- replaced 'shell touch' by 'snakemake touch' for step status targets · ecd585c8
  Valentina Galata authored 4 years ago
  
  ecd585c8
- 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
- made original plasflow output tmp · 8e79e0b3
  Valentina Galata authored 4 years ago
  
  8e79e0b3
- updated slurm.config: plasflow should run on bigmem · a9ce46ad
  Valentina Galata authored 4 years ago
  
  a9ce46ad
- minor updates and bug fixes; added minced jar to its rule (issue #42 ) · 118b6afd
  Valentina Galata authored 4 years ago
  
  118b6afd
- readme update · 693fafd2
  Valentina Galata authored 4 years ago
  
  693fafd2
- added rule to install minced (issue #42 ) · 83464353
  Valentina Galata authored 4 years ago
  
  83464353
- added minced as submodule (issue #42 ) · 0729f6f8
  Valentina Galata authored 4 years ago
  
  0729f6f8
- new rules to setup tools/data; added casc installation (issue #41 ) · 2ac06d02
  Valentina Galata authored 4 years ago
  
  2ac06d02
- added casc as submodule (issue #41 ) · 19531951
  Valentina Galata authored 4 years ago
  
  19531951
- added conda YAML for mmseqs2 · 53e5cbd7
  Valentina Galata authored 4 years ago
  
  53e5cbd7
- minor change in conda YAML for cd-hit · 52ee688c
  Valentina Galata authored 4 years ago
  
  52ee688c
- rm old conda YAML for cd-hit · 60ed5480
  Valentina Galata authored 4 years ago
  
  60ed5480