Commits · 00fa74c216e589dae0998b6beb58a356f0991da0 · Dominik Brilhaus / Facultative CAM in Talinum

Mar 19, 2025
- improve logic to gather output directories from kallisto scatter step · 00fa74c2
  Dominik Brilhaus authored 3 weeks ago
  
  00fa74c2
Mar 18, 2025
- towards combining everything in one arc.cwl · ff506329
  Dominik Brilhaus authored 3 weeks ago
  
  ff506329
- rename assay rnaseq · 12952600
  Dominik Brilhaus authored 3 weeks ago
  
  12952600
- add cwl docs · d154be9e
  Dominik Brilhaus authored 3 weeks ago
  
  d154be9e
- switch kallisto input to array of records · 943e5e52
  Dominik Brilhaus authored 3 weeks ago
  
  943e5e52
- add and run fastqc workflow · 43934494
  Dominik Brilhaus authored 3 weeks ago
  
  43934494
Mar 17, 2025
- cleaning · 988ac506
  Dominik Brilhaus authored 3 weeks ago
  
  988ac506
- convert shiny to single-step cwl · f099f06d
  Dominik Brilhaus authored 3 weeks ago
  
  f099f06d
- start to cwl-wrap shiny app · 0f5de5cb
  Dominik Brilhaus authored 3 weeks ago
  
  0f5de5cb
Mar 14, 2025
- rename workflow to sleuth · c572b83d
  Dominik Brilhaus authored 4 weeks ago
  
  c572b83d
- rm deprecated isa merge · 62287362
  Dominik Brilhaus authored 4 weeks ago
  
  62287362
- rm deprecated sleuth approach · 77cbdcf9
  Dominik Brilhaus authored 4 weeks ago
  
  77cbdcf9
- fixed kallisto_collect · 12915113
  Dominik Brilhaus authored 4 weeks ago
  
  12915113
- deseq: use csv as input, return svg figures · 9146ed60
  Dominik Brilhaus authored 4 weeks ago
  
  9146ed60
- adapt isaSampleToRawDataSeq to start from Source (not Sample) · 26181b2f
  Dominik Brilhaus authored 4 weeks ago
  
  26181b2f
- try fix kallisto_vollect (fails due to docker deps) · effde36d
  Dominik Brilhaus authored 4 weeks ago
  
  effde36d
- align with spec: kallisto · 693ee201
  Dominik Brilhaus authored 4 weeks ago
  
  693ee201
- remove cwl aux-tools · 7efff571
  Dominik Brilhaus authored 4 weeks ago
  
  7efff571
- align with spec: isaSampleToRawData · be46d9df
  Dominik Brilhaus authored 4 weeks ago
  
  be46d9df
- align with spec: deseq2 (needs fix, missing dep) · 6c9a0b87
  Dominik Brilhaus authored 4 weeks ago
  
  6c9a0b87
Dec 02, 2024
- add email adresses · 0d104868
  Dominik Brilhaus authored 4 months ago
  
  0d104868
Nov 10, 2024
- switch metadata input · 46773aa6
  Dominik Brilhaus authored 5 months ago
  
  46773aa6
Nov 07, 2024
- fix isa sample process reader · a3a1fdb8
  Dominik Brilhaus authored 5 months ago
  
  a3a1fdb8
- rename · 181db967
  Dominik Brilhaus authored 5 months ago
  
  181db967
- allow factor list · 070b5035
  Dominik Brilhaus authored 5 months ago
  
  070b5035
Nov 05, 2024
- deseq cwl works (without docker) · 8a4c41b4
  Dominik Brilhaus authored 5 months ago
  
  8a4c41b4
- towards wrap deseq in cwl · 95b5b5bd
  Dominik Brilhaus authored 5 months ago
  
  95b5b5bd
Nov 04, 2024
- [needs f# fix] add isaSampleToRawDataSeq · 28e57415
  Dominik Brilhaus authored 5 months ago
  
  28e57415
Aug 05, 2024
- add log last run · 0bf45cab
  Dominik Brilhaus authored 8 months ago
  
  0bf45cab
- re-run kallisto with v 0.50 · 449cda92
  Dominik Brilhaus authored 8 months ago
  
  449cda92
- allow to adapt which part of the file name(s) shall be kept · 20f7b1f7
  Dominik Brilhaus authored 8 months ago
  
  20f7b1f7
Aug 02, 2024
- trying to fix use of R with CWL · cb06bbb8
  Dominik Brilhaus authored 8 months ago
  
  cb06bbb8
- kallisto workflow results all samples · 2dbb8cc5
  Dominik Brilhaus authored 8 months ago
  
  2dbb8cc5
- collect results in single folder · 312c4907
  Dominik Brilhaus authored 8 months ago
  
  312c4907
- somewhat generic kallisto with multiple samples worked · 8bc5ebe5
  Dominik Brilhaus authored 8 months ago
  
  8bc5ebe5
- design workflow · e92c3586
  Dominik Brilhaus authored 8 months ago
  
  e92c3586
- first steps re-design cwl based analysis · 9214eb5e
  Dominik Brilhaus authored 8 months ago
  
  9214eb5e
- restructure kallisto pipeline · 68c17471
  Dominik Brilhaus authored 8 months ago
  
  68c17471
- remove old scripts, cwl approaches, run results · 163979ff
  Dominik Brilhaus authored 8 months ago
  
  163979ff
Jan 23, 2024
- re-add large files · 038a57da
  Dominik Brilhaus authored 1 year ago
  
  038a57da