Commits · f8219ccf8c7f35bd6fb01d02a6b538d1e4d1638a · GUDMAP_RBK / RNA-seq

Feb 03, 2020
- Add initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Feb 02, 2020
- Merge branch '5-dedupReads' into 'develop' · a30baa9c
  Gervaise Henry authored 5 years ago
```
Resolve "process_dedup"

Closes #5

See merge request !17
```
  a30baa9c
- Merge resolution · 8d75705f
  Gervaise Henry authored 5 years ago
  
  8d75705f
Jan 30, 2020
- Merge branch '29-fetch.refs.from.s3' into 'develop' · b1770e35
  Venkat Malladi authored 5 years ago
```
Resolve "process_getRef"

Closes #29

See merge request !16
```
  b1770e35
- Fix specie/s in CI · 0bf42fdf
  Gervaise Henry authored 5 years ago
  
  0bf42fdf
- Move endsManual in parseMetadata process from spike to stranded · 6bedccc4
  Gervaise Henry authored 5 years ago
  
  6bedccc4
- Cleanup some ci misses · 529dadea
  Gervaise Henry authored 5 years ago
  
  529dadea
- Updated output file names for unit test. · d16e6c86
  Jonathan Gesell authored 5 years ago
  
  d16e6c86
- RE-specified the output directory. · 91a9ea5f
  Jonathan Gesell authored 5 years ago
  
  91a9ea5f
- Corrected file names · 30349d74
  Jonathan Gesell authored 5 years ago
  
  30349d74
- Corrected input and output BAM file paths. · f2dd8009
  Jonathan Gesell authored 5 years ago
  
  f2dd8009
- Update .gitlab-ci.yml, removed variable IDs. · 06790eb4
  Jonathan Gesell authored 5 years ago
  
  06790eb4
- Added unit testing · a28ab789
  Jonathan Gesell authored 5 years ago
  
  a28ab789
- Put change to parseMeta script to ci also · f49af45e
  Gervaise Henry authored 5 years ago
  
  f49af45e
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix stranded parse and add 8 cores to trimData · 471380f7
  Gervaise Henry authored 5 years ago
  
  471380f7
- Fix ci yml formal · f03e0077
  Gervaise Henry authored 5 years ago
  
  f03e0077
- Fix mus ref loc name · a0cd39f7
  Gervaise Henry authored 5 years ago
  
  a0cd39f7
- 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
- Initial branch commit, tested and working. · 75c31810
  Jonathan Gesell authored 5 years ago
  
  75c31810
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