Commits · 3f71105bb6980899abada414e355db0a82c5db1a · GUDMAP_RBK / RNA-seq

Mar 15, 2020
- Fix spelling errors · 3f71105b
  Venkat Malladi authored 5 years ago
  
  3f71105b
- Added paired end and stranded features to featureCounts. · 387290a1
  Jonathan Gesell authored 5 years ago
  
  387290a1
Mar 09, 2020
- Fix exit for tests in calculateTPM.R · 2c5bbdc1
  Gervaise Henry authored 5 years ago
  
  2c5bbdc1
- Update dag.png · 800dae10
  Gervaise Henry authored 5 years ago
  
  800dae10
- Generalize count column earlier · 35a91ea1
  Gervaise Henry authored 5 years ago
  
  35a91ea1
Mar 08, 2020
- Fix path of script for unit test · b36bb08e
  Gervaise Henry authored 5 years ago
  
  b36bb08e
- Fix docker handle in unit test · 2ab086d2
  Gervaise Henry authored 5 years ago
  
  2ab086d2
- Add unit test for makeFeatureCounts · 88c55e12
  Gervaise Henry authored 5 years ago
  
  88c55e12
- Fix tpm r filename · 9663d913
  Gervaise Henry authored 5 years ago
  
  9663d913
Mar 06, 2020
- Add ulimit to ci integration · 899957ed
  Gervaise Henry authored 5 years ago
  
  899957ed
- Add back process · 14784208
  Gervaise Henry authored 5 years ago
  
  14784208
- TEST remove count process · 96a89c3a
  Gervaise Henry authored 5 years ago
  
  96a89c3a
- Add TPM calculation to nf · d0d5114b
  Gervaise Henry authored 5 years ago
  
  d0d5114b
- Remove edgeR from calculateTPM script · 1f1c6075
  Gervaise Henry authored 5 years ago
  
  1f1c6075
- Add rscript to calculate tpm · 44e21870
  Gervaise Henry authored 5 years ago
  
  44e21870
- Added feature counts process. · 6675415d
  Jonathan Gesell authored 5 years ago
  
  6675415d
Feb 18, 2020
- Update unit for getRef to use local refs · 75486483
  Gervaise Henry authored 5 years ago
  
  75486483
- Merge branch '39-dev.docs' into 'develop' · 5b436e02
  Venkat Malladi authored 5 years ago
```
Resolve "Update design docs"

Closes #39

See merge request !21
```
  5b436e02
Feb 17, 2020
- Update dag.png · 4862704a
  Gervaise Henry authored 5 years ago
  
  4862704a
- Update README.md · c6fc3b0b
  Gervaise Henry authored 5 years ago
  
  c6fc3b0b
- Update gitlab bug and merge request templates · 30fc41fb
  Gervaise Henry authored 5 years ago
  
  30fc41fb
- Make integration_pe create dag and make artifact · 0d895b2c
  Gervaise Henry authored 5 years ago
  
  0d895b2c
- Update readme with dag · d27e0c58
  Gervaise Henry authored 5 years ago
  
  d27e0c58
- Add DAG · 77749b88
  Gervaise Henry authored 5 years ago
  
  77749b88
- Use dedup for bw · 7cbce1fc
  Gervaise Henry authored 5 years ago
  
  7cbce1fc
- Remove premature rseqc references · ff70cf7f
  Gervaise Henry authored 5 years ago
  
  ff70cf7f
- Update readme · bc73cf59
  Gervaise Henry authored 5 years ago
  
  bc73cf59
- Update process table · 5e9236a3
  Gervaise Henry authored 5 years ago
  
  5e9236a3
- Update flowchart pdf · 2c0d9f11
  Gervaise Henry authored 5 years ago
  
  2c0d9f11
- Update flowchart · 6f15d988
  Gervaise Henry authored 5 years ago
  
  6f15d988
Feb 15, 2020
- Merge branch '8-makeBigWig' into 'develop' · 00144f10
  Gervaise Henry authored 5 years ago
```
Resolve "process_makeBigWig"

Closes #8

See merge request !19
```
  00144f10
Feb 14, 2020
- Updated queues for some processes based on observed resource usage. · c1d6c6f6
  Jonathan Gesell authored 5 years ago
  
  c1d6c6f6
Feb 12, 2020
- Update .gitlab-ci.yml · ff7f8483
  Jonathan Gesell authored 5 years ago
  
  ff7f8483
- Update .gitlab-ci.yml · 3dff84f8
  Jonathan Gesell authored 5 years ago
  
  3dff84f8
- Updated to include reference selection · d9895270
  Jonathan Gesell authored 5 years ago
  
  d9895270
Feb 11, 2020
- Merge branch '8-makeBigWig' of git.biohpc.swmed.edu:gudmap_rbk/rna-seq into 8-makeBigWig · dcb7aee4
  Jonathan Gesell authored 5 years ago
```
"Merging local branch with online work."
```
  dcb7aee4
- Corrected path for hisat2 with new directory names · 00643d40
  Jonathan Gesell authored 5 years ago
  
  00643d40
Feb 10, 2020
- Corrected typo in .gitlab-ci.yml · 73a6b3d6
  Jonathan Gesell authored 5 years ago
  
  73a6b3d6
- Update .gitlab-ci.yml · 819e87c2
  Jonathan Gesell authored 5 years ago
  
  819e87c2
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