Commits · cc3de64136e55af8f352cc8c77f0a7440ebcee9c · GUDMAP_RBK / RNA-seq

Aug 13, 2020
- 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
- Fix getRefs to use super · 8ea08743
  Gervaise Henry authored 4 years ago
  
  8ea08743
- Fix splitStudy for slurm · 48768cfe
  Gervaise Henry authored 4 years ago
  
  48768cfe
- Run all getRefs on super (runniung by study overutilizes local) · 4c9dff21
  Gervaise Henry authored 4 years ago
  
  4c9dff21
- Allow study script to run on cluster · 894a5f84
  Gervaise Henry authored 4 years ago
  
  894a5f84
- Increase delay between study initiated runs to 30s · 97f69442
  Gervaise Henry authored 4 years ago
  
  97f69442
- Change unit test for trim to match new setting · b86fdcca
  Gervaise Henry authored 4 years ago
  
  b86fdcca
- Make by study script run nextflow with quiet flag · 412d92df
  Gervaise Henry authored 4 years ago
  
  412d92df
- 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
- Put 10sec delay between study launch + 25 parallel · 2a494f04
  Gervaise Henry authored 4 years ago
  
  2a494f04
- Add unit test for outputBag · d65d19ec
  Gervaise Henry authored 4 years ago
  
  d65d19ec
- Add inital output bag creation · 49e3be49
  Gervaise Henry authored 4 years ago
  
  49e3be49
- Ouput inputBag · 0bdfdeef
  Gervaise Henry authored 4 years ago
  
  0bdfdeef
Aug 11, 2020
- Version to 0.0.1 · 8a8ce097
  Gervaise Henry authored 4 years ago
  
  8a8ce097
Aug 10, 2020
- Merge branch 'new.qc.out' into 'develop' · fe51a743
  Venkat Malladi authored 4 years ago
```
Metadata output update

Closes #56 and #52

See merge request !36
```
  fe51a743
- Convert string to int for range checking in consistency test · 6341ca53
  Gervaise Henry authored 4 years ago
  
  6341ca53
- Change consistence test from exact match to within 1/100,000 change from expected · ade9acec
  Gervaise Henry authored 4 years ago
  
  ade9acec
- Update dag · 506a006b
  Gervaise Henry authored 4 years ago
  
  506a006b
- Convert gene symbols to EntrezID in count/tpm table · c41b4788
  Gervaise Henry authored 4 years ago
  
  c41b4788
Aug 08, 2020
- Add instructions for running from study RID · c99ba0ab
  Gervaise Henry authored 4 years ago
  
  c99ba0ab
- Add scripts to run from study RID · 158a687e
  Gervaise Henry authored 4 years ago
  
  158a687e
Aug 07, 2020
- Add rounding to numbers in multiqc table · 8dd59f38
  Gervaise Henry authored 4 years ago
  
  8dd59f38
Aug 06, 2020
- Fix tin table in multiqc · 66da5252
  Gervaise Henry authored 4 years ago
  
  66da5252
- Remove quotes and colons from multiqc custom tables · e0b3d4bd
  Gervaise Henry authored 4 years ago
  
  e0b3d4bd
- Add quotes to multiqc tables · be4bafc9
  Gervaise Henry authored 4 years ago
  
  be4bafc9
Aug 05, 2020
- Fix raw read output · 254c13bc
  Gervaise Henry authored 4 years ago
  
  254c13bc
- Fix raw count calculation · 1168b330
  Gervaise Henry authored 4 years ago
  
  1168b330
- Fix raw read count to R1 · bb989a48
  Gervaise Henry authored 4 years ago
  
  bb989a48
- Extract raw reads · fa11871a
  Gervaise Henry authored 4 years ago
  
  fa11871a
- Remove dummy fastqc · 4faeddc4
  Gervaise Henry authored 4 years ago
  
  4faeddc4
- Remove number formats from multiqc config · 72e1e94b
  Gervaise Henry authored 4 years ago
  
  72e1e94b
- Change innerDistance removal for SE to SE matadata check · 32b02fa3
  Gervaise Henry authored 4 years ago
  
  32b02fa3
Aug 04, 2020
- Fix assigned read extraction · d7189017
  Gervaise Henry authored 4 years ago
  
  d7189017
- Fixt assignedReads handling · de7d66a6
  Gervaise Henry authored 4 years ago
  
  de7d66a6
- Fix countData unit summary file name · a9b7c868
  Gervaise Henry authored 4 years ago
  
  a9b7c868
- Remove intermediate bash variables · 06983662
  Gervaise Henry authored 4 years ago
  
  06983662
- Fix echo greps · 0eee8782
  Gervaise Henry authored 4 years ago
  
  0eee8782
- Fix assigned reads extraction · 821253a0
  Gervaise Henry authored 4 years ago
  
  821253a0