Commits · 5c9e24e4076d62fccd2ce4c6fb8cbcaad8030277 · GUDMAP_RBK / RNA-seq

Nov 13, 2020
- Update with set for since only 1 variable. Also update pattern to pass files. · 5c9e24e4
  Venkat Malladi authored 4 years ago
  
  5c9e24e4
Nov 12, 2020
- Add back parallel trim step. Moved fastqc step after trim. · 7cf5d610
  Venkat Malladi authored 4 years ago
  
  7cf5d610
Nov 09, 2020
- Add in software versions and references. · 10cd6a4c
  Venkat Malladi authored 4 years ago
  
  10cd6a4c
Oct 31, 2020
- fix typo in name of pipeline. · cd7534b9
  Venkat Malladi authored 4 years ago
  
  cd7534b9
- Update config for email. · 7cf8c4d2
  Venkat Malladi authored 4 years ago
  
  7cf8c4d2
- Test failure. · b8e8774b
  Venkat Malladi authored 4 years ago
  
  b8e8774b
Sep 20, 2020
- Reduce species inference cutoffs · c114a629
  Gervaise Henry authored 4 years ago
  
  0.0.4_indev
  
  c114a629
Sep 14, 2020
- Fix elif · deabc9e6
  Gervaise Henry authored 4 years ago
  
  deabc9e6
- Fix datahub specific bed folder move · cb073c1e
  Gervaise Henry authored 4 years ago
  
  cb073c1e
- Fix ref move after getRef datahub pull · 296ee453
  Gervaise Henry authored 4 years ago
  
  296ee453
- 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
- Add datahub fetch for pipeline · 6ff4315b
  Gervaise Henry authored 4 years ago
  
  6ff4315b
Sep 09, 2020
- 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 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
- 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 14, 2020
- Output tpm table · 71f142d5
  Gervaise Henry authored 4 years ago
  
  71f142d5
Aug 13, 2020
- Remove parallelization of trim_galore · 7bcdead3
  Gervaise Henry authored 4 years ago
  
  7bcdead3
- Remove Illumina addapter trim restriction, set to default (auto) and limit cores to 4 · e91b3300
  Gervaise Henry authored 4 years ago
  
  e91b3300
Aug 12, 2020
- Add inital output bag creation · 49e3be49
  Gervaise Henry authored 4 years ago
  
  49e3be49
- Ouput inputBag · 0bdfdeef
  Gervaise Henry authored 4 years ago
  
  0bdfdeef
Aug 10, 2020
- Convert gene symbols to EntrezID in count/tpm table · c41b4788
  Gervaise Henry authored 4 years ago
  
  c41b4788
Aug 07, 2020
- Add rounding to numbers in multiqc table · 8dd59f38
  Gervaise Henry authored 4 years ago
  
  8dd59f38