Commits · bbaa391b8b42b9f1df41d8e37d2645db746eada4 · GUDMAP_RBK / RNA-seq

Feb 07, 2020
- Merge branch '8-makeBigWig' of git.biohpc.swmed.edu:gudmap_rbk/rna-seq into 8-makeBigWig · bbaa391b
  Jonathan Gesell authored 5 years ago
```
Merge in the pytests for makeBigWig
```
  bbaa391b
- Added pytest for makeBigWig. · 9363735e
  Jonathan Gesell authored 5 years ago
  
  9363735e
- Update .gitlab-ci.yml · 5d2d6ef6
  Jonathan Gesell authored 5 years ago
  
  5d2d6ef6
- Update .gitlab-ci.yml · 9f4b63ed
  Jonathan Gesell authored 5 years ago
  
  9f4b63ed
- Update .gitlab-ci.yml to include makeBigWig step. · 26d11700
  Jonathan Gesell authored 5 years ago
  
  26d11700
Feb 04, 2020
- Merge branch '9-fastqc' into 'develop' · eac0a7c5
  Venkat Malladi authored 5 years ago
```
Resolve "process_fastqc"

Closes #9

See merge request !18
```
  eac0a7c5
- Fix fastqc pytest name · 645546fa
  Gervaise Henry authored 5 years ago
  
  645546fa
Feb 03, 2020
- Add resources to AWS configs · 850d99f8
  Gervaise Henry authored 5 years ago
  
  850d99f8
- Fix outdir for fastqc ci and process · 4ca7cd19
  Gervaise Henry authored 5 years ago
  
  4ca7cd19
- Write fastqc output in current dir for ci · 2735b0c4
  Gervaise Henry authored 5 years ago
  
  2735b0c4
- Add fastqc output · 2503d937
  Gervaise Henry authored 5 years ago
  
  2503d937
- Add CI for fastqc · 8f580cc7
  Gervaise Henry authored 5 years ago
  
  8f580cc7
- 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