Commits · 502120745a3c177457a5e75ffb8a254cb640a68b · GUDMAP_RBK / RNA-seq

Feb 14, 2020
- Fix pytest for new getData unit · 50212074
  Gervaise Henry authored 5 years ago
  
  50212074
- Test bdbag fetch on text file · de33d175
  Gervaise Henry authored 5 years ago
  
  de33d175
- Fix if not exist in bdbagFetch.sh · 66591ecd
  Gervaise Henry authored 5 years ago
  
  66591ecd
- Fix if not exist in bdbagFetch.sh · cf08008a
  Gervaise Henry authored 5 years ago
  
  cf08008a
- Fix if not exist in bdbagFetch.sh · 42a16c69
  Gervaise Henry authored 5 years ago
  
  42a16c69
- CI unit: getRef cp local, getData test version of script to fetch txt · 61cc48e6
  Gervaise Henry authored 5 years ago
  
  61cc48e6
Feb 12, 2020
- Updated to include reference selection · d9895270
  Jonathan Gesell authored 5 years ago
  
  d9895270
Feb 11, 2020
- Corrected path for hisat2 with new directory names · 00643d40
  Jonathan Gesell authored 5 years ago
  
  00643d40
- Add local ref · df73c7e9
  Gervaise Henry authored 5 years ago
  
  df73c7e9
Feb 10, 2020
- Fix temp comment out reference s3 bucket · bf9d4f71
  Gervaise Henry authored 5 years ago
  
  bf9d4f71
- Add temp local ref location · 770f2860
  Gervaise Henry authored 5 years ago
  
  770f2860
- Add ascii art · 4c87cdef
  Gervaise Henry authored 5 years ago
  
  4c87cdef
Feb 07, 2020
- Added pytest for makeBigWig. · 9363735e
  Jonathan Gesell authored 5 years ago
  
  9363735e
Feb 04, 2020
- Fix fastqc pytest name · 645546fa
  Gervaise Henry authored 5 years ago
  
  645546fa
Feb 03, 2020
- Add resources to AWS configs · 850d99f8
  Gervaise Henry authored 5 years ago
  
  850d99f8
- 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 CI for fastqc · 8f580cc7
  Gervaise Henry authored 5 years ago
  
  8f580cc7
- 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
- Updated output file names for unit test. · d16e6c86
  Jonathan Gesell authored 5 years ago
  
  d16e6c86
- Added unit testing · a28ab789
  Jonathan Gesell authored 5 years ago
  
  a28ab789
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix stranded parse and add 8 cores to trimData · 471380f7
  Gervaise Henry authored 5 years ago
  
  471380f7
- 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 28, 2020
- Remove line testing. As count_lines doesn't work for bam and bai files · 2333e8b4
  Venkat Malladi authored 5 years ago
  
  2333e8b4
- Fix the actual tests · e94986e1
  Venkat Malladi authored 5 years ago
  
  e94986e1
- Change single-end tests to reference correct experiment file. · 6b1e233a
  Venkat Malladi authored 5 years ago
  
  6b1e233a
- Update read comparison and decorator · dbdf865f
  Venkat Malladi authored 5 years ago
  
  dbdf865f
Jan 27, 2020
- Update test_alignReads.py · a3564b7c
  Jonathan Gesell authored 5 years ago
  
  a3564b7c
Jan 24, 2020
- Update workflow/tests/test_alignReads.py · 398747a6
  Jonathan Gesell authored 5 years ago
```
Deleted workflow/tests/test_align.py
```
  398747a6
- Updated test scripts. · de4d2b8b
  Jonathan Gesell authored 5 years ago
  
  de4d2b8b
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added utils.py · 88a757f3
  Jonathan Gesell authored 5 years ago
  
  88a757f3
- 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