Commits · af133ded00f62498fb6238a043ef660c2750301a · GUDMAP_RBK / RNA-seq

Mar 20, 2020
- initial commit, untested · af133ded
  Jonathan Gesell authored 5 years ago
  
  af133ded
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
- Add back and update name of reference for inferMeta · e187976f
  Gervaise Henry authored 5 years ago
  
  e187976f
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
- 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
- Add unit test for inferMetadata · a2a809c7
  Gervaise Henry authored 5 years ago
  
  a2a809c7
- Remove R aggregation · ac21c821
  Gervaise Henry authored 5 years ago
  
  ac21c821
- Clean inference, add tin · 12996d71
  Gervaise Henry authored 5 years ago
  
  12996d71
Feb 28, 2020
- Mod some infer meta · 4a68865f
  Gervaise Henry authored 5 years ago
  
  4a68865f
Feb 17, 2020
- Remove premature rseqc references · ff70cf7f
  Gervaise Henry authored 5 years ago
  
  ff70cf7f
Feb 14, 2020
- Add infer_experiment.py · 3c12e9c1
  Gervaise Henry authored 5 years ago
  
  3c12e9c1
- Fix pytest for new getData unit · 50212074
  Gervaise Henry authored 5 years ago
  
  50212074
- Test bdbag fetch on text file · de33d175
  Gervaise Henry authored 5 years ago
  
  de33d175
- Fix if not exist in bdbagFetch.sh · 66591ecd
  Gervaise Henry authored 5 years ago
  
  66591ecd
- Fix if not exist in bdbagFetch.sh · cf08008a
  Gervaise Henry authored 5 years ago
  
  cf08008a
- Fix if not exist in bdbagFetch.sh · 42a16c69
  Gervaise Henry authored 5 years ago
  
  42a16c69
- Updated queues for some processes based on observed resource usage. · c1d6c6f6
  Jonathan Gesell authored 5 years ago
  
  c1d6c6f6
- CI unit: getRef cp local, getData test version of script to fetch txt · 61cc48e6
  Gervaise Henry authored 5 years ago
  
  61cc48e6
Feb 12, 2020
- Updated to include reference selection · d9895270
  Jonathan Gesell authored 5 years ago
  
  d9895270
Feb 11, 2020
- Corrected path for hisat2 with new directory names · 00643d40
  Jonathan Gesell authored 5 years ago
  
  00643d40
- Add local ref · df73c7e9
  Gervaise Henry authored 5 years ago
  
  df73c7e9
Feb 10, 2020
- Fix temp comment out reference s3 bucket · bf9d4f71
  Gervaise Henry authored 5 years ago
  
  bf9d4f71
- Add temp local ref location · 770f2860
  Gervaise Henry authored 5 years ago
  
  770f2860
- Add ascii art · 4c87cdef
  Gervaise Henry authored 5 years ago
  
  4c87cdef
Feb 07, 2020
- Added pytest for makeBigWig. · 9363735e
  Jonathan Gesell authored 5 years ago
  
  9363735e
Feb 04, 2020
- 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
- Add fastqc output · 2503d937
  Gervaise Henry authored 5 years ago
  
  2503d937