Commits · de4d2b8bd28459bbb9ef1b41800cf5bcb918c6a2 · GUDMAP_RBK / RNA-seq

Jan 24, 2020
- Updated test scripts. · de4d2b8b
  Jonathan Gesell authored 5 years ago
  
  de4d2b8b
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added utils.py · 88a757f3
  Jonathan Gesell authored 5 years ago
  
  88a757f3
- 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
- Corrected scope-specific error in parseMeta.py · ca261a6b
  Jonathan Gesell authored 5 years ago
  
  ca261a6b
- 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
- Merge develop into align branch · 7c677cf1
  Gervaise Henry authored 5 years ago
  
  7c677cf1
- Initial run for align. · fa22c087
  Jonathan Gesell authored 5 years ago
  
  fa22c087
- Initial run for align. · 04c4e3da
  Jonathan Gesell authored 5 years ago
  
  04c4e3da
- Merge branch '2-process_createManifest' into 'develop' · 1c3a166b
  Venkat Malladi authored 5 years ago
```
Resolve "process_createManifest"

Closes #2

See merge request !14
```
  1c3a166b
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
- Ignore FutureWarnings · 714c61bc
  Gervaise Henry authored 5 years ago
  
  714c61bc
- Ignore FutureWarnings · 9081851f
  Gervaise Henry authored 5 years ago
  
  9081851f
- Fix endsManual · e7eaeaa4
  Gervaise Henry authored 5 years ago
  
  e7eaeaa4
- Fix fastq # test · 70ce7af1
  Gervaise Henry authored 5 years ago
  
  70ce7af1
- Fix len fastqs · fbd2da78
  Gervaise Henry authored 5 years ago
  
  fbd2da78
- Fix undetected meta endness · 29f36785
  Gervaise Henry authored 5 years ago
  
  29f36785
- Keep meta endness separate · bce4b6ea
  Gervaise Henry authored 5 years ago
  
  bce4b6ea
- Add to unit test for endManual · 0f709935
  Gervaise Henry authored 5 years ago
  
  0f709935
- 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
- Merge develop into branch · 41a2c611
  Gervaise Henry authored 5 years ago
  
  41a2c611
- Add unit test for parseMetadata · 8c5b5a80
  Gervaise Henry authored 5 years ago
  
  8c5b5a80
- Add unit test for parseMetadata · 07007f49
  Gervaise Henry authored 5 years ago
  
  07007f49
- Parse metadata · e32cb502
  Gervaise Henry authored 5 years ago
  
  e32cb502