Commits · 5ee1ac2c7bc81fff4296fa702a7c729d3a007026 · GUDMAP_RBK / RNA-seq

Mar 24, 2020
- Add getRefInfer · 5ee1ac2c
  Gervaise Henry authored 4 years ago
  
  5ee1ac2c
- Change unit test for downsampleData singularity to exec · 48c69997
  Gervaise Henry authored 4 years ago
  
  48c69997
- Add unit test for downsampleData · 8e3cf6c4
  Gervaise Henry authored 4 years ago
  
  8e3cf6c4
- Add dowsampling trimmed fastqs · 3b4d0255
  Gervaise Henry authored 4 years ago
  
  3b4d0255
Mar 23, 2020
- Updata design docs · 7e0d0e5d
  Gervaise Henry authored 4 years ago
  
  7e0d0e5d
Mar 21, 2020
- Merge branch '6-processCounts' into 'develop' · fe73c982
  Venkat Malladi authored 4 years ago
```
Resolve "process_count"

See merge request !22
```
  fe73c982
Mar 20, 2020
- Updated exit message. · 5acdbca8
  Venkat Malladi authored 4 years ago
  
  5acdbca8
- Corrected typo in makeFeatureCounts test. · 7d2108a5
  Jonathan Gesell authored 4 years ago
  
  7d2108a5
- Code review changes/corrections · 28f1a97f
  Jonathan Gesell authored 4 years ago
  
  28f1a97f
Mar 19, 2020
- Reverted to using SLURM with super queue. · 47e9c3e6
  Jonathan Gesell authored 4 years ago
  
  47e9c3e6
- Changed executor to local for inferMetaData to attempt to run quicker. · 810cfffb
  Jonathan Gesell authored 4 years ago
  
  810cfffb
Mar 18, 2020
- Improved logging and removal of redundant variables. · 1e445926
  Jonathan Gesell authored 5 years ago
  
  1e445926
Mar 16, 2020
- Merge resolution · 03aa79a9
  Gervaise Henry authored 5 years ago
  
  03aa79a9
- Changed tag from 'gene_id' to 'gene_name' · 3c9c7d4d
  Jonathan Gesell authored 5 years ago
  
  3c9c7d4d
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
- Merge branch '35-RSeQC' into 'develop' · ad35f8df
  Venkat Malladi authored 5 years ago
```
Resolve "process_RSeQC"

Closes #35

See merge request !23
```
  ad35f8df
- Update dag.png · 0c28e8d2
  Gervaise Henry authored 5 years ago
  
  0c28e8d2
Mar 14, 2020
- Fix reference input for inferMeta · f774a99c
  Gervaise Henry authored 5 years ago
  
  f774a99c
- Fix dedupBam input of inferMeta · 2beb83ad
  Gervaise Henry authored 5 years ago
  
  2beb83ad
- Use dedupBam for inferMeta · ca8ec578
  Gervaise Henry authored 5 years ago
  
  ca8ec578
- Removed unused script · e5fdb858
  Gervaise Henry authored 5 years ago
  
  e5fdb858
- Update dag.png · cedf49d7
  Gervaise Henry authored 5 years ago
  
  cedf49d7
- Fix mkdir bdbag in ci · 68224f63
  Gervaise Henry authored 5 years ago
  
  68224f63
- Add back and update name of reference for inferMeta · e187976f
  Gervaise Henry authored 5 years ago
  
  e187976f
- Merge branch 'develop' into '35-RSeQC' · 575c554d
  Gervaise Henry authored 5 years ago
```
# Conflicts:
#   .gitlab-ci.yml
#   workflow/conf/biohpc.config
```
  575c554d
Mar 13, 2020
- Fix trim qc output · 23cfdc21
  Gervaise Henry authored 5 years ago
  
  23cfdc21
- Fix dedup qc output · 31054b21
  Gervaise Henry authored 5 years ago
  
  31054b21
- Add process log files · 1f7e1dc9
  Gervaise Henry authored 5 years ago
  
  1f7e1dc9
- Include optional inner distance histogram data output · 765e5226
  Gervaise Henry authored 5 years ago
  
  765e5226
- Update design docs · 6da4a7d1
  Gervaise Henry authored 5 years ago
  
  6da4a7d1
- Output align bam/bai to tuple, use rawBam for inference, fix failed read · 57220b3a
  Gervaise Henry authored 5 years ago
  
  57220b3a
Mar 12, 2020
- Fix sillier error in align unit ci pytest · 420cede9
  Gervaise Henry authored 5 years ago
  
  420cede9
- Fix silly error in align unit ci pytest · ac502364
  Gervaise Henry authored 5 years ago
  
  ac502364
- Fix deduped unit ci sorted bam/bai prefix · 1e50ff6e
  Gervaise Henry authored 5 years ago
  
  1e50ff6e
- Add bai test to dedup unit ci pytest · f50feedd
  Gervaise Henry authored 5 years ago
  
  f50feedd
- Fix bai in align unit ci pytest · c076037b
  Gervaise Henry authored 5 years ago
  
  c076037b
- Fix bam indexing output name to .bam.bai · 70e6fa19
  Gervaise Henry authored 5 years ago
  
  70e6fa19
- Fix tin input in unit CO · 3e7d2beb
  Gervaise Henry authored 5 years ago
  
  3e7d2beb
- Add unit test for inferMetadata · a2a809c7
  Gervaise Henry authored 5 years ago
  
  a2a809c7