Commits · 28a9d3ffee6963d436d173c3542c1022e975199f · GUDMAP_RBK / RNA-seq

Feb 11, 2021
- Nextflow-ify · 28a9d3ff
  Gervaise Henry authored 4 years ago
  
  28a9d3ff
- Nextflow-ify · 0a4b00a6
  Gervaise Henry authored 4 years ago
  
  0a4b00a6
Jan 25, 2021
- Merge data error pre-Execution run · 77410b76
  Gervaise Henry authored 4 years ago
  
  77410b76
- Add blank mRNA_QC on data fail · f4e88555
  Gervaise Henry authored 4 years ago
  
  f4e88555
Jan 20, 2021
- Make sampled align use > 32GB nodes on BioHPC · 9e121dac
  Gervaise Henry authored 4 years ago
  
  9e121dac
- Add premature fail execution run upload with fastq file error · 94dac4ed
  Gervaise Henry authored 4 years ago
  
  94dac4ed
Jan 15, 2021
- Add in missinng process config. · fa009e23
  Venkat Malladi authored 4 years ago
  
  fa009e23
- Update biohpc.config · 73490420
  Venkat Malladi authored 4 years ago
  
  73490420
Jan 08, 2021
- Fix time param · 57423462
  Gervaise Henry authored 4 years ago
  
  57423462
- Add 4hr time limit for all processes (biohpc.config) · a57f7e87
  Gervaise Henry authored 4 years ago
  
  a57f7e87
- Add 1 retry to all processes · e2773496
  Gervaise Henry authored 4 years ago
  
  e2773496
Jan 07, 2021
- Add retries to all data-hub processes for biohpc config · 2d9e2523
  Gervaise Henry authored 4 years ago
  
  2d9e2523
Jan 05, 2021
- Alow 1 retry of getData and trimData · 02d4766e
  Gervaise Henry authored 4 years ago
  
  02d4766e
- Fix fail pre execution run · 52b950a6
  Gervaise Henry authored 4 years ago
  
  52b950a6
- Use larger nodes for trim process · a1127c20
  Gervaise Henry authored 4 years ago
  
  a1127c20
Jan 04, 2021
- Add fail process to configs · 68acfa31
  Gervaise Henry authored 4 years ago
  
  68acfa31
Jan 03, 2021
- Add finalize execution run and add new references using bag · 57834f48
  Gervaise Henry authored 4 years ago
  
  57834f48
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