Commits · 4ca7cd19546c0c6000e1cffa5d3d94fec5682712 · GUDMAP_RBK / RNA-seq

Feb 03, 2020
- Fix outdir for fastqc ci and process · 4ca7cd19
  Gervaise Henry authored 5 years ago
  
  4ca7cd19
- Add fastqc output · 2503d937
  Gervaise Henry authored 5 years ago
  
  2503d937
- Add initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Jan 30, 2020
- Move endsManual in parseMetadata process from spike to stranded · 6bedccc4
  Gervaise Henry authored 5 years ago
  
  6bedccc4
- Cleanup some ci misses · 529dadea
  Gervaise Henry authored 5 years ago
  
  529dadea
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix ci to use downsampled data · 0d58c090
  Gervaise Henry authored 5 years ago
  
  0d58c090
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
- Initial branch commit, tested and working. · 75c31810
  Jonathan Gesell authored 5 years ago
  
  75c31810
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added files necessary for CI of output files. · dda7cf97
  Jonathan Gesell authored 5 years ago
  
  dda7cf97
- Added indexing step to align, verified output files. · 724ecd45
  Jonathan Gesell authored 5 years ago
  
  724ecd45
Jan 22, 2020
- Manually specifying reference directory, need to automate. Also added... · 19918779
  Jonathan Gesell authored 5 years ago
```
Manually specifying reference directory, need to automate.  Also added remaining flags to paired-end align.
```
  19918779
- Updated Hisat2 options, and output of parseMeta. · d92d93f9
  Jonathan Gesell authored 5 years ago
  
  d92d93f9
- Reverted to ensure that Trim step is functional. · 25502c3d
  Jonathan Gesell authored 5 years ago
  
  25502c3d
- Reverted to ensure that Trim step is functional. · f6c9944a
  Jonathan Gesell authored 5 years ago
  
  f6c9944a
Jan 21, 2020
- Actually fixed references · ebb7239c
  Jonathan Gesell authored 5 years ago
  
  ebb7239c
- Updated references location to more universal location · 4c68aa57
  Jonathan Gesell authored 5 years ago
  
  4c68aa57
- Make metadata values inputs in downstream processes · bd3f9cb1
  Gervaise Henry authored 5 years ago
  
  bd3f9cb1
- Initial run for align. · 04c4e3da
  Jonathan Gesell authored 5 years ago
  
  04c4e3da
Jan 20, 2020
- Change parseMeta to csv ouput · 32aae481
  Gervaise Henry authored 5 years ago
  
  32aae481
Jan 19, 2020
- Add ends used to log · 960e0e4f
  Gervaise Henry authored 5 years ago
  
  960e0e4f
- Make quotes matching · aeaeda5a
  Gervaise Henry authored 5 years ago
  
  aeaeda5a
- Add quotes around endsMeta test · 9d8a1032
  Gervaise Henry authored 5 years ago
  
  9d8a1032
- Remove set ends in trimData · b1330359
  Gervaise Henry authored 5 years ago
  
  b1330359
- Fix replication of ends · 7b6f7324
  Gervaise Henry authored 5 years ago
  
  7b6f7324
- Fix endsManual log · c876602e
  Gervaise Henry authored 5 years ago
  
  c876602e
- Fix len fastqs · fbd2da78
  Gervaise Henry authored 5 years ago
  
  fbd2da78
- Keep meta endness separate · bce4b6ea
  Gervaise Henry authored 5 years ago
  
  bce4b6ea
- Add manual detection of endness if not stored · 0acf38a4
  Gervaise Henry authored 5 years ago
  
  0acf38a4
Jan 18, 2020
- Remove ends output from trimData · c2b81c7c
  Gervaise Henry authored 5 years ago
  
  c2b81c7c
- Fix script as input for parseMetadata · 96626502
  Gervaise Henry authored 5 years ago
  
  96626502
- Fix script as input for parseMetadata · fd0b7c01
  Gervaise Henry authored 5 years ago
  
  fd0b7c01
- Add unit test for parseMetadata · 07007f49
  Gervaise Henry authored 5 years ago
  
  07007f49
- Parse metadata · e32cb502
  Gervaise Henry authored 5 years ago
  
  e32cb502
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
- Give trim_galore all cpu's available · 81cb8e68
  Gervaise Henry authored 5 years ago
  
  81cb8e68
- Make .nf scripts more readable · 131b5517
  Gervaise Henry authored 5 years ago
  
  131b5517
- Make bdbag scripts an input · 43935dd7
  Gervaise Henry authored 5 years ago
  
  43935dd7
- Remove executor settings in .nf · 0ecf1945
  Gervaise Henry authored 5 years ago
  
  0ecf1945