Commits · 4557af34fa8a23c4f86365f088d019b8b0a13131 · Susheel Busi / COSMIC2

Oct 13, 2020
- Upload New File · 4557af34
  Laura Denies authored 4 years ago
  
  4557af34
- Upload New File · 60f8cdc0
  Laura Denies authored 4 years ago
  
  60f8cdc0
- Upload New File · 2b3fd1e4
  Laura Denies authored 4 years ago
  
  2b3fd1e4
- Upload New File · a6a98229
  Laura Denies authored 4 years ago
  
  a6a98229
- Add new directory · e8f7b57e
  Laura Denies authored 4 years ago
  
  e8f7b57e
- Add new directory · b805d02c
  Laura Denies authored 4 years ago
  
  b805d02c
Sep 25, 2020
- Update parse_kaiju.py · 49766e03
  Susheel Busi authored 4 years ago
  
  49766e03
Aug 03, 2020
- adjusted kaiju parsing script · 4778282f
  Susheel Busi authored 4 years ago
  
  4778282f
Aug 02, 2020
- script for parsing the kaiju output/summary file · 3fd096f4
  Susheel Busi authored 4 years ago
  
  3fd096f4
- added the '-e' flag to expand viral taxonomies · 3d3f0a8a
  Susheel Busi authored 4 years ago
  
  3d3f0a8a
- added Kaiju rules and updates to all files · 66bdaaba
  Susheel Busi authored 4 years ago
  
  66bdaaba
Jul 30, 2020
- added the vcontact2 parsing python script · b4b2ecc5
  Susheel Busi authored 4 years ago
  
  b4b2ecc5
- added parameters for kraken · dcc7b637
  Susheel Busi authored 4 years ago
  
  dcc7b637
- updated snakefile with kraken2 rules · f4c69b00
  Susheel Busi authored 4 years ago
  
  f4c69b00
Jul 25, 2020
- working vcontact2 snakefile with associated changes · 677f02a9
  Susheel Busi authored 4 years ago
  
  677f02a9
Jul 24, 2020
- Merge branch 'master' of https://git-r3lab.uni.lu/susheel.busi/cosmic2 · 08d7e4c9
  Susheel Busi authored 4 years ago
  
  08d7e4c9
- vcontact2 changed from v0.9.17 to v0.9.18 · 933f8763
  Susheel Busi authored 4 years ago
  
  933f8763
- Update snakefile · 4f09d42a
  Susheel Busi authored 4 years ago
  
  4f09d42a
- updated the snakefile and run_snakemake files to include updated vibrant · cc65a0ad
  Susheel Busi authored 4 years ago
  
  cc65a0ad
Jul 16, 2020
- Update get_HGT_contig_ID.sh · ae33e231
  Susheel Busi authored 4 years ago
  
  ae33e231
- script to retrieve ORIGINAL contigIDs and their locations based on HGT events... · e2e53b7f
  Susheel Busi authored 4 years ago
  
  script to retrieve ORIGINAL contigIDs and their locations based on HGT events identified by MetaCHIP
  e2e53b7f
Jul 11, 2020
- adding kraken rules and snakefile · 9b69a5e4
  Susheel Busi authored 4 years ago
  
  9b69a5e4
Jul 01, 2020
- updated the snakefile for correctness of files · 5c998c0d
  Susheel Busi authored 4 years ago
  
  5c998c0d
- changed the vibrant walltime and ncpus for improved SLURM scheduling · 94ce6b5f
  Susheel Busi authored 4 years ago
  
  94ce6b5f
Jun 30, 2020
- cluster.json file updated for all rules · 984c0b64
  Susheel Busi authored 4 years ago
  
  984c0b64
- updated snakefile with vcontact2 rules · 5239f3ad
  Susheel Busi authored 4 years ago
  
  5239f3ad
- conda environment for vContact2 · bb9c7cbd
  Susheel Busi authored 4 years ago
  
  bb9c7cbd
- reverting to old scikit-learn due to conflicts · 9c2d4984
  Susheel Busi authored 4 years ago
  
  9c2d4984
- updated the scikit-learn requirement · f0e91bf8
  Susheel Busi authored 4 years ago
  
  f0e91bf8
- edited the snakefile to get the directory stucture for vibrant correct · c0150b0c
  Susheel Busi authored 4 years ago
  
  c0150b0c
- updated the targets based on VIBRANT's output · fd80d91f
  Susheel Busi authored 4 years ago
  
  fd80d91f
Jun 29, 2020
- samples list for vibrant. Does not include C118 due to missing V6 · 3ccd2ee4
  Susheel Busi authored 4 years ago
  
  3ccd2ee4
- snakefile and related files to run vibrant on cosmic data · fe4620e9
  Susheel Busi authored 4 years ago
  
  fe4620e9
Jun 07, 2020
- Update METACHIP.yaml · 07412bb0
  Susheel Busi authored 4 years ago
  
  07412bb0
- Add new file · d265df1d
  Susheel Busi authored 4 years ago
  
  d265df1d
- Add new file · 2a4b61c2
  Susheel Busi authored 4 years ago
  
  2a4b61c2
Feb 24, 2020
- Update FIGURE_LAYOUT_COSMIC.R · db76f013
  Susheel Busi authored 5 years ago
  
  db76f013
- Upload New File · 61400f7e
  Susheel Busi authored 5 years ago
  
  61400f7e
- Add CHANGELOG · 47b999bc
  Susheel Busi authored 5 years ago
  
  47b999bc
- Upload New File · b0a8f207
  Susheel Busi authored 5 years ago
  
  b0a8f207