Commits · 788a539ff9f16263fc0610f744fbca42bb4e160c · GUDMAP_RBK / RNA-seq

Aug 04, 2020
- Extract assigned reads count · 788a539f
  Gervaise Henry authored 4 years ago
  
  788a539f
- Round median TIN to 2 dp · 740d2eff
  Gervaise Henry authored 4 years ago
  
  740d2eff
Aug 03, 2020
- Calculate median TIN and display in report · 5e2e8f64
  Gervaise Henry authored 4 years ago
  
  5e2e8f64
Jul 23, 2020
- AWS Batch works · 9fe16dfb
  Gervaise Henry authored 4 years ago
  
  9fe16dfb
May 01, 2020
- Fix report order · 608bc755
  Gervaise Henry authored 4 years ago
  
  608bc755
- Add metadata and repRID to multiqc report · 3bc88431
  Gervaise Henry authored 4 years ago
  
  3bc88431
Apr 30, 2020
- Add all reports(except metadata) · 4e0779da
  Gervaise Henry authored 4 years ago
  
  4e0779da
Apr 25, 2020
- Change pipeline tracking to curl · ef4ac234
  Gervaise Henry authored 4 years ago
  
  ef4ac234
Apr 22, 2020
- Remove processes from AWS configs · 170b0706
  Gervaise Henry authored 4 years ago
  
  170b0706
- Add inference and apply new naming standards · 53c34278
  Gervaise Henry authored 4 years ago
  
  53c34278
Apr 07, 2020
- 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
Mar 24, 2020
- Add dowsampling trimmed fastqs · 3b4d0255
  Gervaise Henry authored 5 years ago
  
  3b4d0255
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 12, 2020
- 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 14, 2020
- Updated queues for some processes based on observed resource usage. · c1d6c6f6
  Jonathan Gesell authored 5 years ago
  
  c1d6c6f6
Feb 12, 2020
- Updated to include reference selection · d9895270
  Jonathan Gesell authored 5 years ago
  
  d9895270
Feb 03, 2020
- Add resources to AWS configs · 850d99f8
  Gervaise Henry authored 5 years ago
  
  850d99f8
- Add initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Jan 29, 2020
- Fix stranded parse and add 8 cores to trimData · 471380f7
  Gervaise Henry authored 5 years ago
  
  471380f7
- 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 21, 2020
- Initial run for align. · 04c4e3da
  Jonathan Gesell authored 5 years ago
  
  04c4e3da
Jan 18, 2020
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
Jan 15, 2020
- Add https_proxy in getBag process · 4227759d
  Gervaise Henry authored 5 years ago
  
  4227759d
- Try removing proxy settings for biohpc nf config · 33f96a38
  Gervaise Henry authored 5 years ago
  
  33f96a38
- Add singularity and proxy settings to biohpc nf config · 279a541b
  Gervaise Henry authored 5 years ago
  
  279a541b
Jan 14, 2020
- Update gudmapfilexfer images to 1.3 in configs · 805ad15f
  Gervaise Henry authored 5 years ago
  
  805ad15f
- Update nextflow configs to include aws · 92951915
  Gervaise Henry authored 5 years ago
  
  92951915
- Fix biohpc config · a6c1385b
  Gervaise Henry authored 5 years ago
  
  a6c1385b
Jan 13, 2020
- Add getData deriva-download of bagit · e552d2e6
  Gervaise Henry authored 5 years ago
  
  e552d2e6
- Get deriva download of bagit started · cbba6901
  Gervaise Henry authored 5 years ago
  
  cbba6901
Jan 06, 2020
- Added Hisat2 alignment step. Also made files transferable via links. · 76102f6c
  Jonathan Gesell authored 5 years ago
  
  76102f6c
Jan 03, 2020
- Initial branch commit · 19195674
  Jonathan Gesell authored 5 years ago
  
  19195674
Dec 09, 2019
- Upgrade docker images (gudmaprbkfilexfer and trimgalore) to 1.1 · 0147ece8
  Gervaise Henry authored 5 years ago
  
  0147ece8
Nov 11, 2019
- Update biohpc.config to use new docker repo name. · b00a62fe
  Jonathan Gesell authored 5 years ago
  
  b00a62fe
- Added trimming step using trimGalore and logging. · 3d8cc5f7
  Jonathan Gesell authored 5 years ago
  
  3d8cc5f7
Nov 08, 2019
- Update biohpc.config · 16e91612
  Jonathan Gesell authored 5 years ago
  
  16e91612