Commits · 07f363a3fc79be944aa00c350ce3a457cb9910f9 · ESB / ONT_pilot_gitlab · GitLab

30 Jun, 2020 9 commits
- renamed report/ into workflow_report/ · 07f363a3
  Valentina Galata authored Jun 30, 2020
  
  07f363a3
- cleaned up report Snakefile · 9bc1f4e1
  Valentina Galata authored Jun 30, 2020
  
  9bc1f4e1
- added rgi to the report (issue #27 ) · 3838040f
  Valentina Galata authored Jun 30, 2020
  
  3838040f
- link to main conda YAML · 624e0671
  Valentina Galata authored Jun 30, 2020
  
  624e0671
- added configs for GDB (same as the ones in config/); mv sbatch.sh to config/ (issue #45 ) · 7ccc3d89
  Valentina Galata authored Jun 30, 2020
  
  7ccc3d89
- added workflow to create multi-fast5 files; added configs for Zymo-GridION-EVEN-BB-SN (issue #45 ) · afd8885b
  Valentina Galata authored Jun 30, 2020
  
  afd8885b
- added quast and plasflow to report (issue #27 ) · f6e245e7
  Valentina Galata authored Jun 30, 2020
  
  f6e245e7
- fixed a type in analysis.smk (rules/steps) in target paths · 37c82d2b
  Valentina Galata authored Jun 30, 2020
  
  37c82d2b
- analysis step update: updated quast/bbmap/cdhit conda YAML; other minor updates · 7bc8732e
  Valentina Galata authored Jun 30, 2020
  
  7bc8732e
29 Jun, 2020 2 commits
- sbatch.sh -- more cores for the pipeline · 3a97208b
  Valentina Galata authored Jun 29, 2020
  
  3a97208b
- minor fix of regi setup rule · e403f026
  Valentina Galata authored Jun 29, 2020
  
  e403f026
26 Jun, 2020 21 commits
- rm CHANGELOG and not used config · 941b430d
  Valentina Galata authored Jun 26, 2020
  
  941b430d
- updated/added messages to rules; rgi db is loaded in sep. rule · 10e83e92
  Valentina Galata authored Jun 26, 2020
  
  10e83e92
- replaced 'shell touch' by 'snakemake touch' for step status targets · ecd585c8
  Valentina Galata authored Jun 26, 2020
  
  ecd585c8
- updated prodigal runtime in slurm.yaml · 2955bc7d
  Valentina Galata authored Jun 26, 2020
  
  2955bc7d
- minor updates in config.yaml · 9ab20570
  Valentina Galata authored Jun 26, 2020
  
  9ab20570
- made original plasflow output tmp · 8e79e0b3
  Valentina Galata authored Jun 26, 2020
  
  8e79e0b3
- updated slurm.config: plasflow should run on bigmem · a9ce46ad
  Valentina Galata authored Jun 26, 2020
  
  a9ce46ad
- minor updates and bug fixes; added minced jar to its rule (issue #42 ) · 118b6afd
  Valentina Galata authored Jun 26, 2020
  
  118b6afd
- readme update · 693fafd2
  Valentina Galata authored Jun 26, 2020
  
  693fafd2
- added rule to install minced (issue #42 ) · 83464353
  Valentina Galata authored Jun 26, 2020
  
  83464353
- added minced as submodule (issue #42 ) · 0729f6f8
  Valentina Galata authored Jun 26, 2020
  
  0729f6f8
- new rules to setup tools/data; added casc installation (issue #41 ) · 2ac06d02
  Valentina Galata authored Jun 26, 2020
  
  2ac06d02
- added casc as submodule (issue #41 ) · 19531951
  Valentina Galata authored Jun 26, 2020
  
  19531951
- added conda YAML for mmseqs2 · 53e5cbd7
  Valentina Galata authored Jun 26, 2020
  
  53e5cbd7
- minor change in conda YAML for cd-hit · 52ee688c
  Valentina Galata authored Jun 26, 2020
  
  52ee688c
- rm old conda YAML for cd-hit · 60ed5480
  Valentina Galata authored Jun 26, 2020
  
  60ed5480
- new conda YAML for cd-hit · ef74e76a
  Valentina Galata authored Jun 26, 2020
  
  ef74e76a
- rm not used conda YAML files · 178b0e99
  Valentina Galata authored Jun 26, 2020
  
  178b0e99
- conda YAML files for casc and minced (issue #41 and #42 ) · a7dbe097
  Valentina Galata authored Jun 26, 2020
  
  a7dbe097
- bug fixes for rgi and plasflow rules · ca0db4f5
  Valentina Galata authored Jun 26, 2020
  
  ca0db4f5
- updated gitignore · 0e6bf7f1
  Valentina Galata authored Jun 26, 2020
  
  0e6bf7f1
25 Jun, 2020 8 commits
- report: minor update · 2d314da5
  Valentina Galata authored Jun 25, 2020
  
  2d314da5
- updared diamond env (old one could not be build) · 12366758
  Valentina Galata authored Jun 25, 2020
  
  12366758
- updared rgi env (old one could not be build) · 99f85045
  Valentina Galata authored Jun 25, 2020
  
  99f85045
- report: initial setup · 46662031
  Valentina Galata authored Jun 25, 2020
  
  46662031
- config and slurm update · b5077eb7
  Valentina Galata authored Jun 25, 2020
  
  b5077eb7
- mv r.yml in report/ · a2b4e48f
  Valentina Galata authored Jun 25, 2020
  
  a2b4e48f
- report: incl rmarkdown in r.yaml · 7908eb43
  Valentina Galata authored Jun 25, 2020
  
  7908eb43
- mv figures.yml to config/ · 89ac6906
  Valentina Galata authored Jun 25, 2020
  
  89ac6906