Commits · 719bd9f5c0271c3a9e843fd7a22847af5a87adb2 · GUDMAP_RBK / RNA-seq

Sep 14, 2020
- Add refName to getRef · 719bd9f5
  Gervaise Henry authored 4 years ago
  
  719bd9f5
Sep 13, 2020
- Fix pulled ref mv · b25ebe4e
  Gervaise Henry authored 4 years ago
  
  b25ebe4e
- Move bed only on non ERCC · af4b5d04
  Gervaise Henry authored 4 years ago
  
  af4b5d04
- Add search for ERCC ref · 778044bc
  Gervaise Henry authored 4 years ago
  
  778044bc
- Combine inputs for getRefInfer · b123b09a
  Gervaise Henry authored 4 years ago
  
  b123b09a
- Remove collect for getRefInfer · fe197fce
  Gervaise Henry authored 4 years ago
  
  fe197fce
- Use channel · 7a0560f5
  Gervaise Henry authored 4 years ago
  
  7a0560f5
- Add extractRefData.py as channel · 42048773
  Gervaise Henry authored 4 years ago
  
  42048773
- Revert each · 8795d7f5
  Gervaise Henry authored 4 years ago
  
  8795d7f5
- Try each refInfer · c8ce8d74
  Gervaise Henry authored 4 years ago
  
  c8ce8d74
- Fix curl query · 8a236b73
  Gervaise Henry authored 4 years ago
  
  8a236b73
- Add refSource to param table · f0cf62ed
  Gervaise Henry authored 4 years ago
  
  f0cf62ed
- Add deriva auth to getRef · 9de3a949
  Gervaise Henry authored 4 years ago
  
  9de3a949
- Update datahub ref download · 2f239170
  Gervaise Henry authored 4 years ago
  
  2f239170
- Update deriva and python containers in config · accde9b7
  Gervaise Henry authored 4 years ago
  
  accde9b7
- Add datahub fetch for pipeline · 6ff4315b
  Gervaise Henry authored 4 years ago
  
  6ff4315b
Sep 12, 2020
- Fix extractRefData arg · 17df0fa5
  Gervaise Henry authored 4 years ago
  
  17df0fa5
Sep 11, 2020
- Change datahub ref ci form get to ls · 0883570c
  Gervaise Henry authored 4 years ago
  
  0883570c
Sep 09, 2020
- Add extractRefData.py · 80718c06
  Gervaise Henry authored 4 years ago
  
  80718c06
- Add param for ref source · 45593829
  Gervaise Henry authored 4 years ago
  
  45593829
Aug 31, 2020
- Add started time to multiqc #77 · 6bc7f30f
  Gervaise Henry authored 4 years ago
```
(cherry picked from commit 927e3ba6)
```
  6bc7f30f
Aug 27, 2020
- Update CHANGELOG.md, workflow/nextflow.config files · 698ec0c7
  Gervaise Henry authored 4 years ago
  
  698ec0c7
Aug 26, 2020
- Add species override · 03e05d4c
  Gervaise Henry authored 4 years ago
  
  03e05d4c
Aug 25, 2020
- Update multiqc run table for reporting convenience #72 · 579959d8
  Gervaise Henry authored 4 years ago
  
  579959d8
- Add fastq override #71 · 5f48c1c1
  Gervaise Henry authored 4 years ago
  
  5f48c1c1
- Allow override for input bagit #61 · 04bbabd5
  Gervaise Henry authored 4 years ago
  
  04bbabd5
Aug 24, 2020
- Update unit test for count #73 · 6e4ad752
  Gervaise Henry authored 4 years ago
  
  6e4ad752
- Add new custom tables to multiqc #72 · 79f7c244
  Gervaise Henry authored 4 years ago
  
  79f7c244
- Update tpm table #73 · d5c23e26
  Gervaise Henry authored 4 years ago
  
  d5c23e26
Aug 19, 2020
- Reall remove unnecessary cols from tpm table · 0bb7f937
  Gervaise Henry authored 4 years ago
  
  0bb7f937
Aug 16, 2020
- Fix Entrez name · 9924e777
  Gervaise Henry authored 4 years ago
  
  9924e777
Aug 15, 2020
- Remove unnecessary columns on tpm table · 85e676b1
  Gervaise Henry authored 4 years ago
  
  85e676b1
Aug 14, 2020
- Output tpm table · 71f142d5
  Gervaise Henry authored 4 years ago
  
  71f142d5
Aug 13, 2020
- Remove resume from study run (only 1 resume per folder allowed) · ca045a6e
  Gervaise Henry authored 4 years ago
  
  ca045a6e
- Add resume to by study · aa74f9f8
  Gervaise Henry authored 4 years ago
  
  aa74f9f8
- Revert study split to 5 parallel runs · 4a8af8be
  Gervaise Henry authored 4 years ago
  
  4a8af8be
- Revert study split to 5 parallel runs 15sec break · 535d6908
  Gervaise Henry authored 4 years ago
  
  535d6908
- Turn off run logs · cc3de641
  Gervaise Henry authored 4 years ago
  
  cc3de641
- Remove parallelization of trim_galore · 7bcdead3
  Gervaise Henry authored 4 years ago
  
  7bcdead3
- Run getData on super · 2ed81fb6
  Gervaise Henry authored 4 years ago
  
  2ed81fb6