Commits · edd49982b2d75c86922010b4b77a2c1f6faf07de · GUDMAP_RBK / RNA-seq

Feb 28, 2021
- Merge dnanexus changes · edd49982
  Gervaise Henry authored 4 years ago
  
  edd49982
Feb 24, 2021
- Fix nf reference in ci · 94d3aaaa
  Gervaise Henry authored 4 years ago
  
  94d3aaaa
- Move nf and confs to match nextflow format · f8eeebc2
  Gervaise Henry authored 4 years ago
  
  f8eeebc2
Feb 23, 2021
- Add back mkdir -p in seqwho unit test · 6e2c01a8
  Gervaise Henry authored 4 years ago
  
  6e2c01a8
- Try removing ./ from seqwho -f in unit test · 91930b4a
  Gervaise Henry authored 4 years ago
  
  91930b4a
- Make dummy dir for plots · 6b2a74d6
  Gervaise Henry authored 4 years ago
  
  6b2a74d6
- Fix seqwho version collection in ci · 7b90b9dc
  Gervaise Henry authored 4 years ago
  
  7b90b9dc
- Use datahub as source for integration_se ci · 3ce1ddf7
  Gervaise Henry authored 4 years ago
  
  3ce1ddf7
- Fix ci lint · ba58c650
  Gervaise Henry authored 4 years ago
  
  ba58c650
- Replace species inference with seqwho · 634fd8a3
  Gervaise Henry authored 4 years ago
  
  634fd8a3
Feb 19, 2021
- Merge branch 'dnanexus' into 'develop' · 4d7e5c98
  Venkat Malladi authored 4 years ago
```
Dnanexus

See merge request !70
```
  4d7e5c98
- 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
- Add test for seq type failure · 50715724
  Gervaise Henry authored 4 years ago
  
  50715724
- Utilize seq type inference from seqwho · 3c5f30fb
  Gervaise Henry authored 4 years ago
  
  3c5f30fb
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
- Add configs and nf to root for nextflow standard · a566d140
  Gervaise Henry authored 4 years ago
  
  a566d140
- 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