Commits · develop · GUDMAP_RBK / RNA-seq

20 Nov, 2020 2 commits
- Merge branch '68-outputBagDetails' into 'develop' · dcda53fd
  Gervaise H. Henry authored Nov 20, 2020
```
Add run details to output bag

Closes #68

See merge request !51
```
  dcda53fd
- Add Jons Syntax Fix · a89eb9f5
  Jeremy Mathews authored Nov 20, 2020
  
  a89eb9f5
19 Nov, 2020 7 commits
- Change it all back · e605a9e7
  Jeremy Mathews authored Nov 19, 2020
  
  e605a9e7
- Fix RID in singularity · 9b9245dc
  Jeremy Mathews authored Nov 19, 2020
  
  9b9245dc
- Fixed RID · 331ce5b8
  Jeremy Mathews authored Nov 19, 2020
  
  331ce5b8
- Gervaise made me do it again · 89af5024
  Jeremy Mathews authored Nov 19, 2020
  
  89af5024
- Gervaise made me do it · e1bded43
  Jeremy Mathews authored Nov 19, 2020
  
  e1bded43
- Add run details to output bag · f4e55f71
  Jeremy Mathews authored Nov 19, 2020
  
  f4e55f71
- Merge branch '65-trim_galore' into 'develop' · 83d47884
  Gervaise H. Henry authored Nov 19, 2020
```
Add back parallel trim step. Moved fastqc step after trim.

Closes #65

See merge request !50
```
  83d47884
14 Nov, 2020 1 commit
- update dag. · 6728b926
  Venkat Malladi authored Nov 14, 2020
  
  6728b926
13 Nov, 2020 6 commits
- Spell correction. · 7e63c86b
  Venkat Malladi authored Nov 13, 2020
  
  7e63c86b
- Update use of includeInputs. · ccfd2d00
  Venkat Malladi authored Nov 13, 2020
  
  ccfd2d00
- Update changes to reflect only the change in order of steps. Fix output files. · c0a39ab8
  Venkat Malladi authored Nov 13, 2020
  
  c0a39ab8
- Fix extra space. · ecf2f89e
  Venkat Malladi authored Nov 13, 2020
  
  ecf2f89e
- Remove pigz parllel option. · baf8ba31
  Venkat Malladi authored Nov 13, 2020
  
  baf8ba31
- Update with set for since only 1 variable. Also update pattern to pass files. · 5c9e24e4
  Venkat Malladi authored Nov 13, 2020
  
  5c9e24e4
12 Nov, 2020 1 commit
- Add back parallel trim step. Moved fastqc step after trim. · 7cf5d610
  Venkat Malladi authored Nov 12, 2020
  
  7cf5d610
11 Nov, 2020 5 commits
- Update bicf_logo.png · 3ccdc626
  Gervaise H. Henry authored Nov 11, 2020
  
  3ccdc626
- Merge branch '78-tool_version' into develop · 0a0b51e4
  Gervaise H. Henry authored Nov 11, 2020
  
  0a0b51e4
- Merge branch '60-consistency_tests' into 'develop' · f232c58b
  Gervaise H. Henry authored Nov 11, 2020
```
Update consistency checks to be fully in python.

Closes #60

See merge request !46
```
  f232c58b
- Fix id in generate versions. · df286d4f
  Venkat Malladi authored Nov 11, 2020
  
  df286d4f
- Fix number of reads that map. · 7950f38f
  Venkat Malladi authored Nov 11, 2020
  
  7950f38f
10 Nov, 2020 13 commits
- Merge branch '78-tool_version' of git.biohpc.swmed.edu:gudmap_rbk/rna-seq into 78-tool_version · 874ffa5f
  Venkat Malladi authored Nov 10, 2020
  
  874ffa5f
- Address typo's and refernces to pipeline. · 43e3a5e0
  Venkat Malladi authored Nov 10, 2020
  
  43e3a5e0
- Fix custom report names for ordering · fb18e579
  Gervaise H. Henry authored Nov 10, 2020
  
  fb18e579
- Try to get software references working · df529e22
  Gervaise H. Henry authored Nov 10, 2020
  
  df529e22
- Fix spelling error · c7178e06
  Venkat Malladi authored Nov 10, 2020
  
  c7178e06
- Test software version/references multiqc custom report ordering · 28f53e77
  Gervaise H. Henry authored Nov 10, 2020
  
  28f53e77
- Merge branch 'develop' into '60-consistency_tests' · 573ff53b
  Gervaise H. Henry authored Nov 10, 2020
```
# Conflicts:
#   .gitlab-ci.yml
```
  573ff53b
- Merge branch '63-on_error' into 'develop' · c54dec24
  Gervaise H. Henry authored Nov 10, 2020
```
Test failure.

Closes #63

See merge request !47
```
  c54dec24
- Fix parsing of json file. · 4a5ac4a9
  Venkat Malladi authored Nov 10, 2020
  
  4a5ac4a9
- Fix consistency check for where it is grabbing. · ded770b2
  Venkat Malladi authored Nov 10, 2020
  
  ded770b2
- Update README.md · 14154ff6
  Gervaise H. Henry authored Nov 10, 2020
  
  14154ff6
- Try to fix order. · 8eb6c76d
  Venkat Malladi authored Nov 10, 2020
  
  8eb6c76d
- Update DAG, links and order of sections. · b20d758a
  Venkat Malladi authored Nov 10, 2020
  
  b20d758a
09 Nov, 2020 5 commits
- Add in yaml files. · b10c1b1d
  Venkat Malladi authored Nov 09, 2020
  
  b10c1b1d
- Fix regex markdups. · 192da4d6
  Venkat Malladi authored Nov 09, 2020
  
  192da4d6
- Fix regex. · 61468bd9
  Venkat Malladi authored Nov 09, 2020
  
  61468bd9
- Change patterns and changelong. · acc08c89
  Venkat Malladi authored Nov 09, 2020
  
  acc08c89
- Bypass markdups exit status of 1. · 0daf719e
  Venkat Malladi authored Nov 09, 2020
  
  0daf719e