Commits · 27a8214ba3863d606065121d997a322c4bf78198 · ESB / ONT_pilot_gitlab · GitLab

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Apr 25, 2020
- config file · 27a8214b
  Susheel Busi authored 4 years ago
  
  27a8214b
- global snakefile · 2defddca
  Susheel Busi authored 4 years ago
  
  2defddca
- created modular parts of the SNAKEFILE for ease of handling and downstream processes · dc8a6b4f
  Susheel Busi authored 4 years ago
  
  dc8a6b4f
Apr 24, 2020
- added parameters for binning · 898bd724
  Susheel Busi authored 4 years ago
  
  898bd724
- new GTDBTK conda environment · f46ee664
  Susheel Busi authored 4 years ago
  
  f46ee664
- updated the GTDBTK.yaml environment with the development version since the... · 18bcb007
  Susheel Busi authored 4 years ago
  
  updated the GTDBTK.yaml environment with the development version since the stable conda version is not working
  18bcb007
Apr 23, 2020
- fixed maxbin errors · 8f00cec7
  Susheel Busi authored 4 years ago
  
  8f00cec7
- fixed symlink errors · c29f1bf0
  Susheel Busi authored 4 years ago
  
  c29f1bf0
- symlinks for the assemblies for BINNING was failing, so updated the symlink command · 81e8ea16
  Susheel Busi authored 4 years ago
  
  81e8ea16
- removed the output for the wrapper rule - MAPPING · 0444d15c
  Susheel Busi authored 4 years ago
  
  0444d15c
- more environments added · 72da4f61
  Susheel Busi authored 4 years ago
  
  72da4f61
- added the proper environments for mapping and binning · d5917fb4
  Susheel Busi authored 4 years ago
  
  d5917fb4
- minor cosmetic changes to the header · a6594d5e
  Susheel Busi authored 4 years ago
  
  a6594d5e
- added the parameters for 'map_long_reads_to_hybrid_contigs_w_minimap2' rule · 84f9c44b
  Susheel Busi authored 4 years ago
  
  84f9c44b
- fixed the hybrid_build_bwa_mem_index rule · c9b3f61b
  Susheel Busi authored 4 years ago
  
  c9b3f61b
- Snakefile ready to test and take over the world · 565ce080
  Susheel Busi authored 4 years ago
  
  565ce080
- moved the Binning part upstream of all rules · aca81c2f
  Susheel Busi authored 4 years ago
  
  aca81c2f
- Final files ready for running the 2018_GDB_ONT analyses · 14a84062
  Susheel Busi authored 4 years ago
  
  14a84062
Apr 22, 2020
- Config file with the merges between SB and CCL's version, for the final SNAKEFILE · 927bf1c6
  Susheel Busi authored 4 years ago
  
  927bf1c6
- Snakefile with hybrid-mapping incorporated into CCL's Snakefile · cc44828f
  Susheel Busi authored 4 years ago
  
  cc44828f
- updated snakefile and new dastool env · 6b3e58f4
  Susheel Busi authored 4 years ago
  
  6b3e58f4
- updated binning config file · 6f9d9772
  Susheel Busi authored 4 years ago
  
  6f9d9772
- included DASTool, CHECKM and GTDBTK for all samples · e2f5de53
  Susheel Busi authored 4 years ago
  
  e2f5de53
- dastool environment for Binning · d562c629
  Susheel Busi authored 4 years ago
  
  d562c629
- updated config file · 494c61ae
  Susheel Busi authored 4 years ago
  
  494c61ae
- Included contamination check and taxonomy for FLYE and MEGAHIT along with metaspades · 12fff15c
  Susheel Busi authored 4 years ago
  
  12fff15c
- config file updates with GTDBTK data paths · 7d445789
  Susheel Busi authored 4 years ago
  
  7d445789
- updated with working GTDBTK paths and commands · 3fafe071
  Susheel Busi authored 4 years ago
  
  3fafe071
- possible final Snakefile for metaspades with WORKING gtdbtk · 4da62d33
  Susheel Busi authored 4 years ago
  
  4da62d33
- Writing CheckM output to file · bb177bcb
  Susheel Busi authored 4 years ago
  
  bb177bcb
Apr 21, 2020
- updated metaspades snakefile and cluster files with working DAS_Tool and CheckM · 233b7f48
  Susheel Busi authored 4 years ago
  
  233b7f48
- checkm files that are required for the bin contamination checks · 398a2b31
  Susheel Busi authored 4 years ago
  
  398a2b31
- updated Snakefile, cluster and config for metaT read mapping · 56248f29
  Susheel Busi authored 4 years ago
  
  56248f29
Apr 20, 2020
- edited the compute genomecov time · 43c3c4e7
  Susheel Busi authored 4 years ago
  
  43c3c4e7
- config for METASPADES binning · 03ebb430
  Susheel Busi authored 4 years ago
  
  03ebb430
- config info for binning FLYE and MEGAHIT · 47f3239a
  Susheel Busi authored 4 years ago
  
  47f3239a
- snakefile for METASPADES binning. Work in progress. · 2acefbb9
  Susheel Busi authored 4 years ago
  
  2acefbb9
- use this for Binning FLYE and MEGAHIT assemblies. To be incorporated into the original Snakefile · bf7f5ad2
  Susheel Busi authored 4 years ago
  
  bf7f5ad2
- edited the cluster info for metaT mapping · 246e8c8c
  Susheel Busi authored 4 years ago
  
  246e8c8c
- updated the metaT details · a0fb6de5
  Susheel Busi authored 4 years ago
  
  a0fb6de5