Commits · 1902055cbcb6a43d22e1d5b65462b5bde73f8a8b · GUDMAP_RBK / RNA-seq

Jan 30, 2020
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix ci to use downsampled data · 0d58c090
  Gervaise Henry authored 5 years ago
  
  0d58c090
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added files necessary for CI of output files. · dda7cf97
  Jonathan Gesell authored 5 years ago
  
  dda7cf97
- Added indexing step to align, verified output files. · 724ecd45
  Jonathan Gesell authored 5 years ago
  
  724ecd45
Jan 22, 2020
- Manually specifying reference directory, need to automate. Also added... · 19918779
  Jonathan Gesell authored 5 years ago
```
Manually specifying reference directory, need to automate.  Also added remaining flags to paired-end align.
```
  19918779
- Updated Hisat2 options, and output of parseMeta. · d92d93f9
  Jonathan Gesell authored 5 years ago
  
  d92d93f9
- Reverted to ensure that Trim step is functional. · 25502c3d
  Jonathan Gesell authored 5 years ago
  
  25502c3d
- Reverted to ensure that Trim step is functional. · f6c9944a
  Jonathan Gesell authored 5 years ago
  
  f6c9944a
Jan 21, 2020
- Actually fixed references · ebb7239c
  Jonathan Gesell authored 5 years ago
  
  ebb7239c
- Updated references location to more universal location · 4c68aa57
  Jonathan Gesell authored 5 years ago
  
  4c68aa57
- Make metadata values inputs in downstream processes · bd3f9cb1
  Gervaise Henry authored 5 years ago
  
  bd3f9cb1
- Initial run for align. · 04c4e3da
  Jonathan Gesell authored 5 years ago
  
  04c4e3da
Jan 20, 2020
- Change parseMeta to csv ouput · 32aae481
  Gervaise Henry authored 5 years ago
  
  32aae481
Jan 19, 2020
- Add ends used to log · 960e0e4f
  Gervaise Henry authored 5 years ago
  
  960e0e4f
- Make quotes matching · aeaeda5a
  Gervaise Henry authored 5 years ago
  
  aeaeda5a
- Add quotes around endsMeta test · 9d8a1032
  Gervaise Henry authored 5 years ago
  
  9d8a1032
- Remove set ends in trimData · b1330359
  Gervaise Henry authored 5 years ago
  
  b1330359
- Fix replication of ends · 7b6f7324
  Gervaise Henry authored 5 years ago
  
  7b6f7324
- Fix endsManual log · c876602e
  Gervaise Henry authored 5 years ago
  
  c876602e
- Fix len fastqs · fbd2da78
  Gervaise Henry authored 5 years ago
  
  fbd2da78
- Keep meta endness separate · bce4b6ea
  Gervaise Henry authored 5 years ago
  
  bce4b6ea
- Add manual detection of endness if not stored · 0acf38a4
  Gervaise Henry authored 5 years ago
  
  0acf38a4
Jan 18, 2020
- Remove ends output from trimData · c2b81c7c
  Gervaise Henry authored 5 years ago
  
  c2b81c7c
- 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
- 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
- Add https_proxy in getBag process · 4227759d
  Gervaise Henry authored 5 years ago
  
  4227759d
Jan 14, 2020
- Add metadata outputs · 7fa5e438
  Gervaise Henry authored 5 years ago
  
  7fa5e438