Commits · eac0a7c5ac7ccd5877691a07bdaf8a100885257e · GUDMAP_RBK / RNA-seq

Feb 03, 2020
- Add initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Jan 29, 2020
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
- Initial branch commit, tested and working. · 75c31810
  Jonathan Gesell authored 5 years ago
  
  75c31810
Jan 21, 2020
- Initial run for align. · 04c4e3da
  Jonathan Gesell authored 5 years ago
  
  04c4e3da
Jan 18, 2020
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
Jan 15, 2020
- Add https_proxy in getBag process · 4227759d
  Gervaise Henry authored 5 years ago
  
  4227759d
- Try removing proxy settings for biohpc nf config · 33f96a38
  Gervaise Henry authored 5 years ago
  
  33f96a38
- Add singularity and proxy settings to biohpc nf config · 279a541b
  Gervaise Henry authored 5 years ago
  
  279a541b
Jan 14, 2020
- Update gudmapfilexfer images to 1.3 in configs · 805ad15f
  Gervaise Henry authored 5 years ago
  
  805ad15f
- Update nextflow configs to include aws · 92951915
  Gervaise Henry authored 5 years ago
  
  92951915
- Fix biohpc config · a6c1385b
  Gervaise Henry authored 5 years ago
  
  a6c1385b
Jan 13, 2020
- Add getData deriva-download of bagit · e552d2e6
  Gervaise Henry authored 5 years ago
  
  e552d2e6
Jan 06, 2020
- Added Hisat2 alignment step. Also made files transferable via links. · 76102f6c
  Jonathan Gesell authored 5 years ago
  
  76102f6c
Jan 03, 2020
- Initial branch commit · 19195674
  Jonathan Gesell authored 5 years ago
  
  19195674
Dec 09, 2019
- Upgrade docker images (gudmaprbkfilexfer and trimgalore) to 1.1 · 0147ece8
  Gervaise Henry authored 5 years ago
  
  0147ece8
Nov 11, 2019
- Update biohpc.config to use new docker repo name. · b00a62fe
  Jonathan Gesell authored 5 years ago
  
  b00a62fe
- Added trimming step using trimGalore and logging. · 3d8cc5f7
  Jonathan Gesell authored 5 years ago
  
  3d8cc5f7
Nov 08, 2019
- Update biohpc.config · 16e91612
  Jonathan Gesell authored 5 years ago
  
  16e91612
Oct 28, 2019
- Temporary fix for file naming · b89416b5
  Jonathan Gesell authored 5 years ago
  
  b89416b5
Oct 16, 2019
- Add new process to split bdbag by replicates for parallel getData · 347d8e1a
  Gervaise Henry authored 5 years ago
  
  347d8e1a
Oct 15, 2019
- Corrected Singularity CacheDir · 2b4b2e9b
  Jonathan Gesell authored 5 years ago
  
  2b4b2e9b
- Added container functionality · c54a846c
  Jonathan Gesell authored 5 years ago
  
  c54a846c
Oct 08, 2019
- getData setup · e8e5d140
  Gervaise Henry authored 5 years ago
  
  e8e5d140