Commits · bf7f5ad2cc63be954c1ff8e71b440459f5383109 · ESB / ONT_pilot_gitlab

Apr 20, 2020
- 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
- added the metaT processing steps · 0fefca16
  Susheel Busi authored 4 years ago
  
  0fefca16
Apr 19, 2020
- minor changes · f5d53edb
  Susheel Busi authored 4 years ago
  
  f5d53edb
- added tidyverse and cowplot · fab689d5
  Susheel Busi authored 4 years ago
  
  fab689d5
- updated R environment file · f71bf5c8
  Susheel Busi authored 4 years ago
  
  f71bf5c8
- changes to dependencies · c61dc3a0
  Susheel Busi authored 4 years ago
  
  c61dc3a0
- adding updated files. Files for moving results folder, making... · 1991001e
  Susheel Busi authored 4 years ago
  
  adding updated files. Files for moving results folder, making mmseq_upset_plots and a test mmseq_snakefile
  1991001e
Apr 18, 2020
- updated Snakefile · 34f7c373
  Susheel Busi authored 4 years ago
  
  34f7c373
Apr 16, 2020
- updated 'interactive' and 'batch' cpus to bigmem due to occupied CPUs in the other two · c9495426
  Susheel Busi authored 4 years ago
  
  c9495426
Apr 15, 2020
- updates to mmseq2 section made · 08570367
  Susheel Busi authored 4 years ago
  
  08570367
Mar 25, 2020
- Merge branch 'work' into 'master' · e37d28c4
  Susheel Busi authored 5 years ago
  
  Work See merge request susheel.busi/ont_pilot_gitlab!16
  e37d28c4
- changes to mmseq2 config options, i.e threads · 8ae8b9c3
  Susheel Busi authored 5 years ago
  
  8ae8b9c3
- changes to mmseq2 cluster options · 53962f7d
  Susheel Busi authored 5 years ago
  
  53962f7d
- Merge branch 'work' into 'master' · 1a8eed7e
  Susheel Busi authored 5 years ago
  
  changes to mmseq2 rules See merge request susheel.busi/ont_pilot_gitlab!15
  1a8eed7e
- changes to mmseq2 rules · a7376fd3
  Susheel Busi authored 5 years ago
  
  a7376fd3
- Merge branch 'work' into 'master' · 052ee7dd
  Susheel Busi authored 5 years ago
  
  added rules for running MMSEQ2 comparisons See merge request susheel.busi/ont_pilot_gitlab!14
  052ee7dd
- added rules for running MMSEQ2 comparisons · 551e2f15
  Susheel Busi authored 5 years ago
  
  551e2f15
Mar 19, 2020
- Merge branch 'work' into 'master' · 3fc72ff4
  Susheel Busi authored 5 years ago
  
  included nanopolish indexing See merge request susheel.busi/ont_pilot_gitlab!13
  3fc72ff4
- included nanopolish indexing · 9ccc29fd
  Susheel Busi authored 5 years ago
  
  9ccc29fd
Mar 18, 2020
- Merge branch 'work' into 'master' · 48310e12
  Susheel Busi authored 5 years ago
  
  Work See merge request susheel.busi/ont_pilot_gitlab!11
  48310e12
- Snakefile updated · d1a9ddb7
  Susheel Busi authored 5 years ago
  
  d1a9ddb7
- minor updates to the gpu_NO_MOD_demux rules · 39fb26ae
  Susheel Busi authored 5 years ago
  
  39fb26ae
- Merge branch 'work' into 'master' · 1293a0bb
  Susheel Busi authored 5 years ago
  
  Work See merge request susheel.busi/ont_pilot_gitlab!10
  1293a0bb
- Snakefile updated with parameters suggested by ONT for GPU_Basecalling · f300d548
  Susheel Busi authored 5 years ago
  
  f300d548
- config.yaml updated with parameters suggested by ONT for GPU_Basecalling · 000ab11d
  Susheel Busi authored 5 years ago
  
  000ab11d
- Merge branch 'work' into 'master' · c6f41cc2
  Susheel Busi authored 5 years ago
  
  added rules for running basecall_qc_merge_NO_MOD.done See merge request susheel.busi/ont_pilot_gitlab!9
  c6f41cc2
- added rules for running basecall_qc_merge_NO_MOD.done · bc33ef69
  Susheel Busi authored 5 years ago
  
  bc33ef69
- Merge branch 'work' into 'master' · 12934a07
  Susheel Busi authored 5 years ago
  
  added rules for running NanoStat on basecalled files without any methylation modifications See merge request susheel.busi/ont_pilot_gitlab!8
  12934a07
- added rules for running NanoStat on basecalled files without any methylation modifications · edcc592d
  Susheel Busi authored 5 years ago
  
  edcc592d
- Merge branch 'work' into 'master' · 6eb1455d
  Susheel Busi authored 5 years ago
  
  'rule all' updated See merge request susheel.busi/ont_pilot_gitlab!7
  6eb1455d
- 'rule all' updated · e6f39dee
  Susheel Busi authored 5 years ago
  
  e6f39dee
Mar 17, 2020
- Merge branch 'work' into 'master' · 2c4d1e8e
  Susheel Busi authored 5 years ago
  
  updated files with NO_MOD .cfg basecalling for comparison See merge request susheel.busi/ont_pilot_gitlab!6
  2c4d1e8e
- updated files with NO_MOD .cfg basecalling for comparison · 3b5b48dd
  Susheel Busi authored 5 years ago
  
  3b5b48dd
- Merge branch 'work' into 'master' · cf26d706
  Susheel Busi authored 5 years ago
  
  updated Snakefile See merge request susheel.busi/ont_pilot_gitlab!5
  cf26d706
- updated Snakefile · 9bb3c44c
  Susheel Busi authored 5 years ago
  
  9bb3c44c
- Merge branch 'work' into 'master' · b770ef95
  Susheel Busi authored 5 years ago
  
  minor changes to line 61 See merge request susheel.busi/ont_pilot_gitlab!4
  b770ef95
- minor changes to line 61 · 0885a890
  Susheel Busi authored 5 years ago
  
  0885a890
- - Update Snakefile · 791f535d
  Susheel Busi authored 5 years ago
  
  - modified Basecalling with the new "Guppy" basecaller config [see config.yaml]
  791f535d