Commits · c02d977abd1a2ca4c4b7d1d5d5f09046a96db5ae · GUDMAP_RBK / RNA-seq

May 06, 2020
- Generalize find fastq after fetch · c02d977a
  Gervaise Henry authored 5 years ago
  
  c02d977a
May 04, 2020
- Change fetched fastq's mv to cv... mv was truncating some files · 0c0407f9
  Gervaise Henry authored 5 years ago
  
  0c0407f9
May 01, 2020
- Add experiment and study rid's to multiqc report · 8c2c17a2
  Gervaise Henry authored 5 years ago
  
  8c2c17a2
Apr 30, 2020
- Add all reports(except metadata) · 4e0779da
  Gervaise Henry authored 5 years ago
  
  4e0779da
Apr 22, 2020
- Add inference and apply new naming standards · 53c34278
  Gervaise Henry authored 5 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
Jan 30, 2020
- 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
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
Jan 23, 2020
- Added utils.py · 88a757f3
  Jonathan Gesell authored 5 years ago
  
  88a757f3
Jan 22, 2020
- Corrected scope-specific error in parseMeta.py · ca261a6b
  Jonathan Gesell authored 5 years ago
  
  ca261a6b
- Updated Hisat2 options, and output of parseMeta. · d92d93f9
  Jonathan Gesell authored 5 years ago
  
  d92d93f9
Jan 20, 2020
- Change parseMeta to csv ouput · 32aae481
  Gervaise Henry authored 5 years ago
  
  32aae481
Jan 19, 2020
- Ignore FutureWarnings · 714c61bc
  Gervaise Henry authored 5 years ago
  
  714c61bc
- Ignore FutureWarnings · 9081851f
  Gervaise Henry authored 5 years ago
  
  9081851f
- Fix endsManual · e7eaeaa4
  Gervaise Henry authored 5 years ago
  
  e7eaeaa4
- Fix fastq # test · 70ce7af1
  Gervaise Henry authored 5 years ago
  
  70ce7af1
- Fix len fastqs · fbd2da78
  Gervaise Henry authored 5 years ago
  
  fbd2da78
- Fix undetected meta endness · 29f36785
  Gervaise Henry authored 5 years ago
  
  29f36785
- Add manual detection of endness if not stored · 0acf38a4
  Gervaise Henry authored 5 years ago
  
  0acf38a4
Jan 18, 2020
- Parse metadata · e32cb502
  Gervaise Henry authored 5 years ago
  
  e32cb502
- Add checks for meta repRID · 710a67d9
  Gervaise Henry authored 5 years ago
  
  710a67d9
- Make bdbag scripts an input · 43935dd7
  Gervaise Henry authored 5 years ago
  
  43935dd7
- Initial code · 2be5d85a
  Gervaise Henry authored 5 years ago
  
  2be5d85a
Jan 14, 2020
- Rename fetched fastqs and fix se/pe · bbcfbd9f
  Gervaise Henry authored 5 years ago
  
  bbcfbd9f
Jan 13, 2020
- Cleanup .nf · d6cee4a5
  Gervaise Henry authored 5 years ago
  
  d6cee4a5
- Add getData deriva-download of bagit · e552d2e6
  Gervaise Henry authored 5 years ago
  
  e552d2e6
Nov 15, 2019
- Generalize file param input for python scripts · 0bd693e4
  Gervaise Henry authored 5 years ago
  
  0bd693e4