Commits · 535d69081025d7f14efd318b69525b413723e127 · GUDMAP_RBK / RNA-seq

Aug 13, 2020
- 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
May 06, 2020
- Fix fastq output name fix · 178ac5c0
  Gervaise Henry authored 4 years ago
  
  178ac5c0
- Fix fastq output name · 77800005
  Gervaise Henry authored 4 years ago
  
  77800005
- Generalize destination filename for fastq qxtraction · a3839184
  Gervaise Henry authored 4 years ago
  
  a3839184
- Generalize find fastq after fetch · c02d977a
  Gervaise Henry authored 4 years ago
  
  c02d977a
May 04, 2020
- Change fetched fastq's mv to cv... mv was truncating some files · 0c0407f9
  Gervaise Henry authored 4 years ago
  
  0c0407f9
May 01, 2020
- Add experiment and study rid's to multiqc report · 8c2c17a2
  Gervaise Henry authored 4 years ago
  
  8c2c17a2
Apr 30, 2020
- Add all reports(except metadata) · 4e0779da
  Gervaise Henry authored 4 years ago
  
  4e0779da
Apr 22, 2020
- Add inference and apply new naming standards · 53c34278
  Gervaise Henry authored 4 years ago
  
  53c34278
Mar 20, 2020
- Updated exit message. · 5acdbca8
  Venkat Malladi authored 5 years ago
  
  5acdbca8
Mar 14, 2020
- Removed unused script · e5fdb858
  Gervaise Henry authored 5 years ago
  
  e5fdb858
Mar 12, 2020
- Clean inference, add tin · 12996d71
  Gervaise Henry authored 5 years ago
  
  12996d71
Mar 09, 2020
- Fix exit for tests in calculateTPM.R · 2c5bbdc1
  Gervaise Henry authored 5 years ago
  
  2c5bbdc1
- Generalize count column earlier · 35a91ea1
  Gervaise Henry authored 5 years ago
  
  35a91ea1
Mar 08, 2020
- Fix tpm r filename · 9663d913
  Gervaise Henry authored 5 years ago
  
  9663d913
Mar 06, 2020
- Remove edgeR from calculateTPM script · 1f1c6075
  Gervaise Henry authored 5 years ago
  
  1f1c6075
- Add rscript to calculate tpm · 44e21870
  Gervaise Henry authored 5 years ago
  
  44e21870
Feb 28, 2020
- Mod some infer meta · 4a68865f
  Gervaise Henry authored 5 years ago
  
  4a68865f
Feb 14, 2020
- 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