Add zymo workflow (!78) · Merge requests · ESB / ONT_pilot_gitlab · GitLab

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Merged Valentina Galata requested to merge zymo into bright_future 4 years ago

Dec 08, 2020
- zymo: config: updated rumen (to match bright_future branch); rm unused zymo configs · 1648784c
  Valentina Galata authored 4 years ago
  
  1648784c
Dec 04, 2020
- zymo: added mummer/dnadiff (issue #111 ) · 932628f9
  Valentina Galata authored 4 years ago
  
  932628f9
Dec 03, 2020
- zymo: genes.R: added kraken2 upsetr plots (issue #111 ) · 89eea41b
  Valentina Galata authored 4 years ago
  
  89eea41b
- zymo: plots based on assembly gene summary table (issue #111 ) · 1f593938
  Valentina Galata authored 4 years ago
  
  1f593938
- report/zymo: utils.R: minor update of func set_tool_order (needed for #111 ) · 2c1b302c
  Valentina Galata authored 4 years ago
  
  2c1b302c
- zymo: get kegg info (kegg api) (issue #111 ) · 8c532157
  Valentina Galata authored 4 years ago
  
  8c532157
Dec 02, 2020
- zymo: config: updated zymo slurm and sbatch files · d5045300
  Valentina Galata authored 4 years ago
  
  d5045300
- zymo: gene summary tab: added best kegg hit (issue #111 ) · 7d2164ad
  Valentina Galata authored 4 years ago
  
  7d2164ad
- zymo: gene summary tab: added gene length (issue #111 ) · dada9d4b
  Valentina Galata authored 4 years ago
  
  dada9d4b
- zymo: updated snakemake (gene summary, issue #111 ) · 1b38a514
  Valentina Galata authored 4 years ago
  
  1b38a514
Dec 01, 2020
- zymo: updated/modified workflow (not finished) · c5a1bf10
  Valentina Galata authored 4 years ago
  
  c5a1bf10
- zymo: linked prodigal and diamond envs · 123a3851
  Valentina Galata authored 4 years ago
  
  123a3851
- zymo: rm ont fast5 api env · cb3431ac
  Valentina Galata authored 4 years ago
  
  cb3431ac
- zymo: rm prodigal and diamond envs · a7ea6e54
  Valentina Galata authored 4 years ago
  
  a7ea6e54
- zymo: rm tmp files on config/zymo · 0ca83cb3
  Valentina Galata authored 4 years ago
  
  0ca83cb3
- zymo: merged with latest bright_future commit (978c9167 ) · 36f40dc5
  Valentina Galata authored 4 years ago
  
  36f40dc5
Nov 13, 2020
- updated environments · dc5c6203
  Susheel Busi authored 4 years ago
  
  dc5c6203
- working snakefile with VG's suggested modiifcations · 6649e41c
  Susheel Busi authored 4 years ago
  
  6649e41c
- updated zymo rules and files · 2ea53754
  Susheel Busi authored 4 years ago
  
  2ea53754
- updated rules for zymo download and prodigal runs · 48189022
  Susheel Busi authored 4 years ago
  
  48189022
- updated folder name · a6093fc4
  Susheel Busi authored 4 years ago
  
  a6093fc4
Nov 10, 2020
- updated rules for running SibeliaZ against zymo · 48f71674
  Susheel Busi authored 4 years ago
  
  48f71674
- updated slurm and Snakefile(s) · b2909663
  Susheel Busi authored 4 years ago
  
  b2909663
- fixed errors · 87e71188
  Susheel Busi authored 4 years ago
  
  87e71188
- final SibeliaZ rule updated · aa3d9acc
  Susheel Busi authored 4 years ago
  
  aa3d9acc
- added rules and config parameters for SibeliaZ · c1f5fce1
  Susheel Busi authored 4 years ago
  
  c1f5fce1
Nov 09, 2020
- conda environment for sibeliaz · 51dc11fa
  Susheel Busi authored 4 years ago
  
  51dc11fa
- Update Snakefile · 3f1e9492
  Susheel Busi authored 4 years ago
  
  3f1e9492
Nov 06, 2020
- Merge branch 'zymo' of https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab into zymo · b6083aaa
  Susheel Busi authored 4 years ago
  
  b6083aaa
- updated Snakefile to fix key errors in rule comparison · 04cf3058
  Susheel Busi authored 4 years ago
  
  04cf3058
- Update Snakefile · 558b5eeb
  Susheel Busi authored 4 years ago
  
  558b5eeb
- Rules for tables to compare different assemblers and their mapping to zymo · 2578f3d8
  Susheel Busi authored 4 years ago
  
  2578f3d8
- Update Snakefile · 3294ef44
  Susheel Busi authored 4 years ago
  
  3294ef44
Nov 05, 2020
- Comparing the headers in comparision of read-type and assembler against zymo · b150f5eb
  Susheel Busi authored 4 years ago
  
  b150f5eb
- 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