Commits · e32cb502e89a8c5ef495908508c5a29895cefaf3 · GUDMAP_RBK / RNA-seq

Jan 18, 2020
- Parse metadata · e32cb502
  Gervaise Henry authored 5 years ago
  
  e32cb502
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
- Initial code · 2be5d85a
  Gervaise Henry authored 5 years ago
  
  2be5d85a
Jan 15, 2020
- Combine trimData CI se/pe into 1 unit test · 947e7543
  Gervaise Henry authored 5 years ago
  
  947e7543
- 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 getData pytest · 05a8f290
  Gervaise Henry authored 5 years ago
  
  05a8f290
- Add pytest for trim · c7ea5cba
  Gervaise Henry authored 5 years ago
  
  c7ea5cba
- Add pytest for getData · 18667028
  Gervaise Henry authored 5 years ago
  
  18667028
- Add pytest for getBag · 9e1a4c88
  Gervaise Henry authored 5 years ago
  
  9e1a4c88
- Add pytest for getBag · ba4f8944
  Gervaise Henry authored 5 years ago
  
  ba4f8944
- Add pytest for getBag · 42517ba5
  Gervaise Henry authored 5 years ago
  
  42517ba5
- Add pytest for getBag · f4a7a9bd
  Gervaise Henry authored 5 years ago
  
  f4a7a9bd
- Fix biohpc config · a6c1385b
  Gervaise Henry authored 5 years ago
  
  a6c1385b
- Add metadata outputs · 7fa5e438
  Gervaise Henry authored 5 years ago
  
  7fa5e438
- Rename fetched fastqs and fix se/pe · bbcfbd9f
  Gervaise Henry authored 5 years ago
  
  bbcfbd9f
Jan 13, 2020
- Cleanup .nf · d6cee4a5
  Gervaise Henry authored 5 years ago
  
  d6cee4a5
- Add getData deriva-download of bagit · e552d2e6
  Gervaise Henry authored 5 years ago
  
  e552d2e6
- Get deriva download of bagit started · cbba6901
  Gervaise Henry authored 5 years ago
  
  cbba6901
Dec 09, 2019
- Upgrade docker images (gudmaprbkfilexfer and trimgalore) to 1.1 · 0147ece8
  Gervaise Henry authored 5 years ago
  
  0147ece8
Nov 15, 2019
- Generalize file param input for python scripts · 0bd693e4
  Gervaise Henry authored 5 years ago
  
  0bd693e4
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 30, 2019
- Updated for concise output files · c2b05eaa
  Jonathan Gesell authored 5 years ago
  
  c2b05eaa
Oct 29, 2019
- Add back working deriva cookie copy (link) · 9c845c6e
  Gervaise Henry authored 5 years ago
  
  9c845c6e
Oct 28, 2019
- Add file rename in fetch.txt to modifyFetch.py · 92f9b500
  Gervaise Henry authored 5 years ago
  
  92f9b500
- 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 11, 2019
- Working version of getData process · ed35a88e
  Gervaise Henry authored 5 years ago
  
  ed35a88e
Oct 08, 2019
- getData setup · e8e5d140
  Gervaise Henry authored 5 years ago
  
  e8e5d140
Sep 12, 2019
- Initial commit with blank repository files · 94bd37e5
  Gervaise Henry authored 5 years ago
  
  94bd37e5