Commits · 43e3a5e060d6b3504e2d7f2c6eaff27698ce862a · GUDMAP_RBK / RNA-seq

Nov 10, 2020
- Address typo's and refernces to pipeline. · 43e3a5e0
  Venkat Malladi authored 4 years ago
  
  43e3a5e0
Nov 09, 2020
- Fix regex markdups. · 192da4d6
  Venkat Malladi authored 4 years ago
  
  192da4d6
- Fix regex. · 61468bd9
  Venkat Malladi authored 4 years ago
  
  61468bd9
- Change patterns and changelong. · acc08c89
  Venkat Malladi authored 4 years ago
  
  acc08c89
- Update Markdups. · 435f3889
  Venkat Malladi authored 4 years ago
  
  435f3889
- Fix output for vrsion of nextflow pipeline. · 9763c0a7
  Venkat Malladi authored 4 years ago
  
  9763c0a7
- Fix output file for versions. · be7ae1f2
  Venkat Malladi authored 4 years ago
  
  be7ae1f2
- remove seqtk and update output for stdout. · 08c58f6f
  Venkat Malladi authored 4 years ago
  
  08c58f6f
- Add in software versions and references. · 10cd6a4c
  Venkat Malladi authored 4 years ago
  
  10cd6a4c
Sep 14, 2020
- Auto pep8'd all python code · 2ec44620
  Gervaise Henry authored 4 years ago
  
  2ec44620
Sep 13, 2020
- Update datahub ref download · 2f239170
  Gervaise Henry authored 4 years ago
  
  2f239170
Sep 12, 2020
- Fix extractRefData arg · 17df0fa5
  Gervaise Henry authored 4 years ago
  
  17df0fa5
Sep 11, 2020
- Change datahub ref ci form get to ls · 0883570c
  Gervaise Henry authored 4 years ago
  
  0883570c
Sep 09, 2020
- Add extractRefData.py · 80718c06
  Gervaise Henry authored 4 years ago
  
  80718c06
Aug 24, 2020
- Update tpm table #73 · d5c23e26
  Gervaise Henry authored 4 years ago
  
  d5c23e26
Aug 19, 2020
- Reall remove unnecessary cols from tpm table · 0bb7f937
  Gervaise Henry authored 4 years ago
  
  0bb7f937
Aug 16, 2020
- Fix Entrez name · 9924e777
  Gervaise Henry authored 4 years ago
  
  9924e777
Aug 15, 2020
- Remove unnecessary columns on tpm table · 85e676b1
  Gervaise Henry authored 4 years ago
  
  85e676b1
Aug 13, 2020
- Remove resume from study run (only 1 resume per folder allowed) · ca045a6e
  Gervaise Henry authored 4 years ago
  
  ca045a6e
- Add resume to by study · aa74f9f8
  Gervaise Henry authored 4 years ago
  
  aa74f9f8
- Revert study split to 5 parallel runs · 4a8af8be
  Gervaise Henry authored 4 years ago
  
  4a8af8be
- Revert study split to 5 parallel runs 15sec break · 535d6908
  Gervaise Henry authored 4 years ago
  
  535d6908
- Fix splitStudy for slurm · 48768cfe
  Gervaise Henry authored 4 years ago
  
  48768cfe
- 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
- Make by study script run nextflow with quiet flag · 412d92df
  Gervaise Henry authored 4 years ago
  
  412d92df
Aug 12, 2020
- Put 10sec delay between study launch + 25 parallel · 2a494f04
  Gervaise Henry authored 4 years ago
  
  2a494f04
Aug 10, 2020
- Convert gene symbols to EntrezID in count/tpm table · c41b4788
  Gervaise Henry authored 4 years ago
  
  c41b4788
Aug 08, 2020
- Add scripts to run from study RID · 158a687e
  Gervaise Henry authored 4 years ago
  
  158a687e
Aug 04, 2020
- Round median TIN to 2 dp · 740d2eff
  Gervaise Henry authored 4 years ago
  
  740d2eff
Aug 03, 2020
- Fix median TIN output · 079a7f6c
  Gervaise Henry authored 4 years ago
  
  079a7f6c
- Calculate median TIN and display in report · 5e2e8f64
  Gervaise Henry authored 4 years ago
  
  5e2e8f64
- Move read length num to str to python script · bfaf76ce
  Gervaise Henry authored 4 years ago
  
  bfaf76ce
- Output read length as str · 42b5b070
  Gervaise Henry authored 4 years ago
  
  42b5b070
- Extract read length from submitter metadata · e8b92b99
  Gervaise Henry authored 4 years ago
  
  e8b92b99
Jul 15, 2020
- Move createTestData to test_data · 460d9e53
  Gervaise Henry authored 4 years ago
  
  460d9e53
Jul 14, 2020
- Add unsorted deduped bam to test_data creation · 7afd0f5e
  Gervaise Henry authored 4 years ago
  
  7afd0f5e
- Fix new CI unit tests · 3da0fb06
  Gervaise Henry authored 4 years ago
  
  3da0fb06
- Add script to create test data · 5f257a20
  Gervaise Henry authored 4 years ago
  
  5f257a20
May 20, 2020
- Fix cp error for fastq names with multiple R1/2 · 0c3d1a1e
  Gervaise Henry authored 4 years ago
  
  0c3d1a1e