Dnanexus (!70) · Merge requests · GUDMAP_RBK / RNA-seq

Merged Dnanexus

dnanexus into develop

Merged Gervaise Henry requested to merge dnanexus into develop 4 years ago

Feb 19, 2021
- Change nextflow run locations for CI to root · 0e05309f
  Gervaise Henry authored 4 years ago
  
  0e05309f
- Merge branch 'develop' into 'dnanexus' · 9c320c12
  Gervaise Henry authored 4 years ago
```
# Conflicts:
#   nextflow.config
#   rna-seq.nf
```
  9c320c12
- Update file refs in .nf to match new locations · 53c18086
  Gervaise Henry authored 4 years ago
  
  53c18086
- Update CHANGELOG · 4d3cbbc9
  Gervaise Henry authored 4 years ago
  
  4d3cbbc9
- Add dnanexusExample.json file · d2f9fcd5
  Gervaise Henry authored 4 years ago
  
  d2f9fcd5
- Update README.md · b82a1a63
  Gervaise Henry authored 4 years ago
  
  b82a1a63
- Add to cleanup · 192320f0
  Gervaise Henry authored 4 years ago
  
  192320f0
- Move non nextflow configs back to workflow and symlink files · 4bd19e37
  Gervaise Henry authored 4 years ago
  
  4bd19e37
Feb 18, 2021
- Fix missing auth file processes · f355c461
  Gervaise Henry authored 4 years ago
  
  f355c461
- Fix align machinetype in d dnanexus config · f309fa46
  Gervaise Henry authored 4 years ago
  
  f309fa46
Feb 16, 2021
- Add cpu/mem to dnanexus config · 78fc6ecc
  Gervaise Henry authored 4 years ago
  
  78fc6ecc
Feb 15, 2021
- Fix bigwig output name pattern · ddb35f4e
  Gervaise Henry authored 4 years ago
  
  ddb35f4e
Feb 13, 2021
- Link deriva credentials for upload processed files and fix logs · 466e814a
  Gervaise Henry authored 4 years ago
  
  466e814a
- Link deriva credentials for upload input/output bags · 9fd3eb5a
  Gervaise Henry authored 4 years ago
  
  9fd3eb5a
Feb 12, 2021
- Move fastq count before cp · 821a0f05
  Gervaise Henry authored 4 years ago
  
  821a0f05
- Change bdbag to use cookie locally · 785c4858
  Gervaise Henry authored 4 years ago
  
  785c4858
- Change symlink to cp for cookie in getData · 3324d1ea
  Gervaise Henry authored 4 years ago
  
  3324d1ea
- Try removing stage-as from getData · 63509f78
  Gervaise Henry authored 4 years ago
  
  63509f78
- Add quotes around find predicate · 36fc4229
  Gervaise Henry authored 4 years ago
  
  36fc4229
- Convert ls to find · bdbe616f
  Gervaise Henry authored 4 years ago
  
  bdbe616f
- Fix input folders to match nf being in base · ede40613
  Gervaise Henry authored 4 years ago
  
  ede40613
- Fix zip name · c630b961
  Gervaise Henry authored 4 years ago
  
  c630b961
- Use predicted name of inputBag zip instead of using ls · ded9c3a1
  Gervaise Henry authored 4 years ago
  
  ded9c3a1
- Remove docker prefix · 24e74af8
  Gervaise Henry authored 4 years ago
  
  24e74af8
- Change containers for dnanexus to have prefix docker:// · 7ba3c17a
  Gervaise Henry authored 4 years ago
  
  7ba3c17a
- Change dnanexus executor · 23ed57ea
  Gervaise Henry authored 4 years ago
  
  23ed57ea
- Add dummy main.nf · e96d1001
  Gervaise Henry authored 4 years ago
  
  e96d1001
Feb 11, 2021
- Fix nf filename · c8a7a5a9
  Gervaise Henry authored 4 years ago
  
  c8a7a5a9
- Nextflow-ify · 28a9d3ff
  Gervaise Henry authored 4 years ago
  
  28a9d3ff
- Nextflow-ify · 0a4b00a6
  Gervaise Henry authored 4 years ago
  
  0a4b00a6
Feb 10, 2021
- Add local configs · 76775df8
  Gervaise Henry authored 4 years ago
  
  76775df8
- Fix datahub ref download · 9d37cf2a
  Gervaise Henry authored 4 years ago
  
  9d37cf2a
Feb 09, 2021
- Add dnanexus configs · ec4e0c7e
  Gervaise Henry authored 4 years ago
  
  ec4e0c7e

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