Commits · d6aef8ebc413a3b9f5b23b4d13d6feb2fd05b14a · ESB / ONT_pilot_gitlab · GitLab

21 Aug, 2020 4 commits
- report: updated names/colors of assemblers in utils.R · d6aef8eb
  Valentina Galata authored Aug 21, 2020
  
  d6aef8eb
- configs: sbatch.sh: run snakemake only if conda env activation has worked · 34ac0857
  Valentina Galata authored Aug 21, 2020
  
  34ac0857
- notes: updated mashmap script · 1b257f12
  Valentina Galata authored Aug 21, 2020
  
  1b257f12
- Update sbatch.sh · 38268814
  Susheel Busi authored Aug 21, 2020
  
  38268814
20 Aug, 2020 2 commits
- Zymo/GSI20 configs: replaced main conda env path · 4ac143ff
  Valentina Galata authored Aug 20, 2020
  
  4ac143ff
- readme update · ea2bddb7
  Valentina Galata authored Aug 20, 2020
  
  ea2bddb7
19 Aug, 2020 5 commits
- notes: mashmap update · 04045c15
  Valentina Galata authored Aug 19, 2020
  
  04045c15
- GIS20/Zymo configs: fixed a typo · 6fa78459
  Valentina Galata authored Aug 19, 2020
  
  6fa78459
- notes: mashmap (issue #35 ) · 015d6d47
  Valentina Galata authored Aug 19, 2020
  
  015d6d47
- updated configs · db86679c
  Valentina Galata authored Aug 19, 2020
  
  db86679c
- polishing update: changed polishing strategy, updated racon conda yaml to... · 1ffcfe82
  Valentina Galata authored Aug 19, 2020
```
polishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)
```
  1ffcfe82
18 Aug, 2020 8 commits
- notes: diamond test (issue #78 ) · dd75bd8f
  Valentina Galata authored Aug 18, 2020
  
  dd75bd8f
- notes: infernal test · c2cd8ebc
  Valentina Galata authored Aug 18, 2020
  
  c2cd8ebc
- report: numbers of cdhit stats (table) · 2659ef18
  Valentina Galata authored Aug 18, 2020
  
  2659ef18
- better expression to list targets for assembly step · fef9a05c
  Valentina Galata authored Aug 18, 2020
  
  fef9a05c
- updated GDB config: added mapping back to the steps · e71b9507
  Valentina Galata authored Aug 18, 2020
  
  e71b9507
- report: update to include new assemblers; fixed tool order in cdhit/diamond plots · f45459a1
  Valentina Galata authored Aug 18, 2020
  
  f45459a1
- mash: rm contig-screen analysis, fixed a bug (not all assemblies included in assembly sketch) · 9df850a2
  Valentina Galata authored Aug 18, 2020
  
  9df850a2
- bbmap/bbduk to rm rrna reads: fixed cmd (issue #49 ) · ffdcc3aa
  Valentina Galata authored Aug 18, 2020
  
  ffdcc3aa
17 Aug, 2020 9 commits
- fixed paths for some mash rules (issue #79 ) · 31a6605d
  Valentina Galata authored Aug 17, 2020
  
  31a6605d
- GIS20/Zymo config: sortmerna/bbmap update · 3df1c26a
  Valentina Galata authored Aug 17, 2020
  
  3df1c26a
- GDB config: sortmerna/bbmap update · 7c16689b
  Valentina Galata authored Aug 17, 2020
  
  7c16689b
- rm rrna reads: replaced sortmerna by bbmap (not tested) (issue #49 ) · 7fc7f4d1
  Valentina Galata authored Aug 17, 2020
  
  7fc7f4d1
- GDB config (slurm): rule mapping_bwa_mem_assembly_hyhy · e3eae03c
  Valentina Galata authored Aug 17, 2020
  
  e3eae03c
- GIS20 configs: updated · 992a11c4
  Valentina Galata authored Aug 17, 2020
  
  992a11c4
- zymo configs: updated · 14c69148
  Valentina Galata authored Aug 17, 2020
  
  14c69148
- changes need to include imp3 assembly (issue #76 ) · 29822190
  Valentina Galata authored Aug 17, 2020
  
  29822190
- cdhit: changed renaming rule (issue #75 ), use '-s2 0.5' (issue #68 ) · 214f07ad
  Valentina Galata authored Aug 17, 2020
  
  214f07ad
16 Aug, 2020 7 commits
- notes: mmseqs2 example call · ae21c8ce
  Valentina Galata authored Aug 16, 2020
  
  ae21c8ce
- GDB config: sormerna update · 88debfb8
  Valentina Galata authored Aug 16, 2020
  
  88debfb8
- preproc step: sortmerna targets only if metat · b64323e5
  Valentina Galata authored Aug 16, 2020
  
  b64323e5
- mapping step: fixed a bug - wrong names for targets · 64fe2ff8
  Valentina Galata authored Aug 16, 2020
  
  64fe2ff8
- updated tax rules: kaiju for all proteins, kraken2 for filtered contigs only · e4c8ebf0
  Valentina Galata authored Aug 16, 2020
  
  e4c8ebf0
- GDB config: sormerna cores and runtime, other minor changes · 7bca601e
  Valentina Galata authored Aug 16, 2020
  
  7bca601e
- GDB config: more cores and time for sortmerna · 3a42ed49
  Valentina Galata authored Aug 16, 2020
  
  3a42ed49
14 Aug, 2020 4 commits
- notes: diamond hits scripts, mmseqs2 script (cdhit alternative) · 5a30755a
  Valentina Galata authored Aug 14, 2020
  
  5a30755a
- updated GDB config files · 48aa5933
  Valentina Galata authored Aug 14, 2020
  
  48aa5933
- added canu conda yaml (issue #72 ) · 9fba72e5
  Valentina Galata authored Aug 14, 2020
  
  9fba72e5
- added sortmerna: preproc rule, mapping rule for sr split into metag/metat... · 3cc031ec
  Valentina Galata authored Aug 14, 2020
```
added sortmerna: preproc rule, mapping rule for sr split into metag/metat (issue #49); mapping rule for hyhy assembly (issue #76)
```
  3cc031ec
13 Aug, 2020 1 commit
- updated assembler names and colors in workflow_report/scripts/utils.R · fe910ac4
  Valentina Galata authored Aug 13, 2020
  
  fe910ac4