Commits · 170b070690f65bdbc2736dd9a6fd95f04dd5df3d · GUDMAP_RBK / RNA-seq

Apr 22, 2020
- Remove processes from AWS configs · 170b0706
  Gervaise Henry authored 4 years ago
  
  170b0706
- Add unit CI test for (new) inferMetadata · c17b8a62
  Gervaise Henry authored 4 years ago
  
  c17b8a62
- Add inference and apply new naming standards · 53c34278
  Gervaise Henry authored 4 years ago
  
  53c34278
Apr 07, 2020
- Reorder processes · 1d48e1ef
  Gervaise Henry authored 4 years ago
  
  1d48e1ef
- Add align sampled data · 2b89cc74
  Gervaise Henry authored 4 years ago
  
  2b89cc74
- Fix nextflow/runner error, change singularity cache, and limit processes in unit ci to 20 · c0adecfd
  Gervaise Henry authored 4 years ago
  
  c0adecfd
Apr 02, 2020
- Fix infer.csv output · cc6ffe96
  Gervaise Henry authored 4 years ago
  
  cc6ffe96
- Update rna-seq.nf · b292ccee
  Gervaise Henry authored 4 years ago
  
  b292ccee
- Update rna-seq.nf · 862e319e
  Gervaise Henry authored 4 years ago
  
  862e319e
Apr 01, 2020
- Changed infer.tsv back to infer.csv with appropriate formatting changes. · 4346896f
  Jonathan Gesell authored 4 years ago
  
  4346896f
Mar 30, 2020
- Used betterd CHRs for tests. · 622ebfca
  Jonathan Gesell authored 5 years ago
  
  622ebfca
Mar 27, 2020
- Update test_dedupReads.py · d0d886a4
  Jonathan Gesell authored 5 years ago
  
  d0d886a4
- Update test_dedupReads.py · f8ab64d0
  Jonathan Gesell authored 5 years ago
  
  f8ab64d0
- Update test_dedupReads.py · 2321e6cc
  Jonathan Gesell authored 5 years ago
  
  2321e6cc
- Update test_dedupReads.py · 12b9d87f
  Jonathan Gesell authored 5 years ago
  
  12b9d87f
- Update test_dedupReads.py to include split, testing chr1, chr2, chr8 · a06578ad
  Jonathan Gesell authored 5 years ago
  
  a06578ad
Mar 26, 2020
- Parallelized inferMetaData's TIN calculation. · 82bac4e7
  Jonathan Gesell authored 5 years ago
  
  82bac4e7
Mar 24, 2020
- Add getRefInfer · 5ee1ac2c
  Gervaise Henry authored 5 years ago
  
  5ee1ac2c
- Add unit test for downsampleData · 8e3cf6c4
  Gervaise Henry authored 5 years ago
  
  8e3cf6c4
- Add dowsampling trimmed fastqs · 3b4d0255
  Gervaise Henry authored 5 years ago
  
  3b4d0255
Mar 23, 2020
- Fix infer logic · 28850994
  Gervaise Henry authored 5 years ago
  
  28850994
Mar 20, 2020
- Updated exit message. · 5acdbca8
  Venkat Malladi authored 5 years ago
  
  5acdbca8
- Code review changes/corrections · 28f1a97f
  Jonathan Gesell authored 5 years ago
  
  28f1a97f
- initial commit, untested · af133ded
  Jonathan Gesell authored 5 years ago
  
  af133ded
Mar 19, 2020
- Reverted to using SLURM with super queue. · 47e9c3e6
  Jonathan Gesell authored 5 years ago
  
  47e9c3e6
- Changed executor to local for inferMetaData to attempt to run quicker. · 810cfffb
  Jonathan Gesell authored 5 years ago
  
  810cfffb
Mar 18, 2020
- Improved logging and removal of redundant variables. · 1e445926
  Jonathan Gesell authored 5 years ago
  
  1e445926
Mar 16, 2020
- 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
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