Commits · ad5bf09ec8f441003438e39b2bf1da5bcb42ce0a · GUDMAP_RBK / RNA-seq

Dec 17, 2020
- Change process output bag name to uploadProcessedFiles · b08a7fc5
  Gervaise Henry authored 4 years ago
  
  b08a7fc5
Dec 14, 2020
- Add Output Bag · bdfd5567
  Gervaise Henry authored 4 years ago
  
  bdfd5567
Dec 07, 2020
- Add upload output bag · ab0e4bb6
  Gervaise Henry authored 4 years ago
  
  ab0e4bb6
Dec 05, 2020
- Add upload mRNA QC · e4b99530
  Gervaise Henry authored 4 years ago
  
  e4b99530
Dec 02, 2020
- Add upload execution run · 62790800
  Gervaise Henry authored 4 years ago
  
  62790800
Nov 30, 2020
- Add uploadInputBag · eb83dee4
  Gervaise Henry authored 4 years ago
  
  eb83dee4
Sep 13, 2020
- Update datahub ref download · 2f239170
  Gervaise Henry authored 4 years ago
  
  2f239170
Sep 09, 2020
- Add param for ref source · 45593829
  Gervaise Henry authored 4 years ago
  
  45593829
Aug 13, 2020
- Run getData on super · 2ed81fb6
  Gervaise Henry authored 4 years ago
  
  2ed81fb6
- Fix getRefs to use super · 8ea08743
  Gervaise Henry authored 4 years ago
  
  8ea08743
- Run all getRefs on super (runniung by study overutilizes local) · 4c9dff21
  Gervaise Henry authored 4 years ago
  
  4c9dff21
Aug 12, 2020
- Add inital output bag creation · 49e3be49
  Gervaise Henry authored 4 years ago
  
  49e3be49
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
- 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 initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Jan 29, 2020
- 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
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