Commits · 9662650248b1e630a8d9a6457158cbeeefb81e7b · GUDMAP_RBK / RNA-seq

Jan 18, 2020
- Fix script as input for parseMetadata · 96626502
  Gervaise Henry authored 5 years ago
  
  96626502
- Fix script as input for parseMetadata · fd0b7c01
  Gervaise Henry authored 5 years ago
  
  fd0b7c01
- Add unit test for parseMetadata · 07007f49
  Gervaise Henry authored 5 years ago
  
  07007f49
- Parse metadata · e32cb502
  Gervaise Henry authored 5 years ago
  
  e32cb502
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
- Give trim_galore all cpu's available · 81cb8e68
  Gervaise Henry authored 5 years ago
  
  81cb8e68
- Make .nf scripts more readable · 131b5517
  Gervaise Henry authored 5 years ago
  
  131b5517
- Fix second trimData unit test · 4d88c335
  Gervaise Henry authored 5 years ago
  
  4d88c335
- Split unit test for trimData to 2 · 44a7326b
  Gervaise Henry authored 5 years ago
  
  44a7326b
- Make bdbag scripts an input · 43935dd7
  Gervaise Henry authored 5 years ago
  
  43935dd7
- Remove executor settings in .nf · 0ecf1945
  Gervaise Henry authored 5 years ago
  
  0ecf1945
- Remove sub-folders from logsDir · f0d25e3c
  Gervaise Henry authored 5 years ago
  
  f0d25e3c
- Set publishData mode to copy · c56354c1
  Gervaise Henry authored 5 years ago
  
  c56354c1
- Remove repRID from inputs and make global · 850b8d68
  Gervaise Henry authored 5 years ago
  
  850b8d68
- 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