Commits · 5e8def409a1d00b0a99db5f5926bb1854dac5a4e · GUDMAP_RBK / RNA-seq

Jan 29, 2020
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
Jan 28, 2020
- Merge branch '4-align' into 'develop' · be3dd19b
  Gervaise Henry authored 5 years ago
```
Resolve "process_align"

Closes #4

See merge request !15
```
  be3dd19b
- Add in change log to say that we made alignment files for user. · 3e44bbc0
  Venkat Malladi authored 5 years ago
  
  3e44bbc0
- Merge branch 'develop' into 4-align · fca8f872
  Venkat Malladi authored 5 years ago
  
  fca8f872
- Remove line testing. As count_lines doesn't work for bam and bai files · 2333e8b4
  Venkat Malladi authored 5 years ago
  
  2333e8b4
- Fix the actual tests · e94986e1
  Venkat Malladi authored 5 years ago
  
  e94986e1
- Change single-end tests to reference correct experiment file. · 6b1e233a
  Venkat Malladi authored 5 years ago
  
  6b1e233a
- Update read comparison and decorator · dbdf865f
  Venkat Malladi authored 5 years ago
  
  dbdf865f
Jan 27, 2020
- Update test_alignReads.py · a3564b7c
  Jonathan Gesell authored 5 years ago
  
  a3564b7c
Jan 24, 2020
- Update .gitlab-ci.yml · c1554d3c
  Jonathan Gesell authored 5 years ago
  
  c1554d3c
- Update workflow/tests/test_alignReads.py · 398747a6
  Jonathan Gesell authored 5 years ago
```
Deleted workflow/tests/test_align.py
```
  398747a6
- Corrected CI file. · 60d6e158
  Jonathan Gesell authored 5 years ago
  
  60d6e158
- Corrected CI file. · 9afa2ee9
  Jonathan Gesell authored 5 years ago
  
  9afa2ee9
- 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
- Deconvolute inputs in flowchart · 1a414a43
  Gervaise Henry authored 5 years ago
  
  1a414a43
- Embed pipeline flowchart into readme.md · bf5264af
  Gervaise Henry authored 5 years ago
  
  bf5264af
- Update flowchart heading · 2dcd6513
  Gervaise Henry authored 5 years ago
  
  2dcd6513
- Updata design documents · 65b32f0e
  Gervaise Henry authored 5 years ago
  
  65b32f0e
- 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