Commits · 6ff4315be7fb907df3d31b450ab5bf4c6c2a4e85 · GUDMAP_RBK / RNA-seq

Sep 13, 2020
- Add datahub fetch for pipeline · 6ff4315b
  Gervaise Henry authored 4 years ago
  
  6ff4315b
Sep 09, 2020
- Add param for ref source · 45593829
  Gervaise Henry authored 4 years ago
  
  45593829
Aug 31, 2020
- Add started time to multiqc #77 · 6bc7f30f
  Gervaise Henry authored 4 years ago
```
(cherry picked from commit 927e3ba6)
```
  6bc7f30f
Aug 26, 2020
- Add species override · 03e05d4c
  Gervaise Henry authored 4 years ago
  
  03e05d4c
Aug 25, 2020
- Update multiqc run table for reporting convenience #72 · 579959d8
  Gervaise Henry authored 4 years ago
  
  579959d8
- Add fastq override #71 · 5f48c1c1
  Gervaise Henry authored 4 years ago
  
  5f48c1c1
- Allow override for input bagit #61 · 04bbabd5
  Gervaise Henry authored 4 years ago
  
  04bbabd5
Aug 24, 2020
- Add new custom tables to multiqc #72 · 79f7c244
  Gervaise Henry authored 4 years ago
  
  79f7c244
- Update tpm table #73 · d5c23e26
  Gervaise Henry authored 4 years ago
  
  d5c23e26
Aug 14, 2020
- Output tpm table · 71f142d5
  Gervaise Henry authored 4 years ago
  
  71f142d5
Aug 13, 2020
- Remove parallelization of trim_galore · 7bcdead3
  Gervaise Henry authored 4 years ago
  
  7bcdead3
- Remove Illumina addapter trim restriction, set to default (auto) and limit cores to 4 · e91b3300
  Gervaise Henry authored 4 years ago
  
  e91b3300
Aug 12, 2020
- Add inital output bag creation · 49e3be49
  Gervaise Henry authored 4 years ago
  
  49e3be49
- Ouput inputBag · 0bdfdeef
  Gervaise Henry authored 4 years ago
  
  0bdfdeef
Aug 10, 2020
- Convert gene symbols to EntrezID in count/tpm table · c41b4788
  Gervaise Henry authored 4 years ago
  
  c41b4788
Aug 07, 2020
- Add rounding to numbers in multiqc table · 8dd59f38
  Gervaise Henry authored 4 years ago
  
  8dd59f38
Aug 06, 2020
- Fix tin table in multiqc · 66da5252
  Gervaise Henry authored 4 years ago
  
  66da5252
- Remove quotes and colons from multiqc custom tables · e0b3d4bd
  Gervaise Henry authored 4 years ago
  
  e0b3d4bd
- Add quotes to multiqc tables · be4bafc9
  Gervaise Henry authored 4 years ago
  
  be4bafc9
Aug 05, 2020
- Fix raw read output · 254c13bc
  Gervaise Henry authored 4 years ago
  
  254c13bc
- Fix raw count calculation · 1168b330
  Gervaise Henry authored 4 years ago
  
  1168b330
- Fix raw read count to R1 · bb989a48
  Gervaise Henry authored 4 years ago
  
  bb989a48
- Extract raw reads · fa11871a
  Gervaise Henry authored 4 years ago
  
  fa11871a
- Remove dummy fastqc · 4faeddc4
  Gervaise Henry authored 4 years ago
  
  4faeddc4
- Change innerDistance removal for SE to SE matadata check · 32b02fa3
  Gervaise Henry authored 4 years ago
  
  32b02fa3
Aug 04, 2020
- Fix assigned read extraction · d7189017
  Gervaise Henry authored 4 years ago
  
  d7189017
- Fixt assignedReads handling · de7d66a6
  Gervaise Henry authored 4 years ago
  
  de7d66a6
- Remove intermediate bash variables · 06983662
  Gervaise Henry authored 4 years ago
  
  06983662
- Fix echo greps · 0eee8782
  Gervaise Henry authored 4 years ago
  
  0eee8782
- Fix assigned reads extraction · 821253a0
  Gervaise Henry authored 4 years ago
  
  821253a0
- Add new metadata extraction to ci · 11a742a3
  Gervaise Henry authored 4 years ago
  
  11a742a3
- Extract assigned reads count · 788a539f
  Gervaise Henry authored 4 years ago
  
  788a539f
- Fix median read length for SE · 3bde1ea0
  Gervaise Henry authored 4 years ago
  
  3bde1ea0
Aug 03, 2020
- Fix measure read length · f99bfd2a
  Gervaise Henry authored 4 years ago
  
  f99bfd2a
- Fix extract median TIN · 64632a63
  Gervaise Henry authored 4 years ago
  
  64632a63
- Calculate median TIN and display in report · 5e2e8f64
  Gervaise Henry authored 4 years ago
  
  5e2e8f64
- Fix input of parse read length · 8a404d50
  Gervaise Henry authored 4 years ago
  
  8a404d50
- Nextflow-ify bash command to extract median read length · 484d48ed
  Gervaise Henry authored 4 years ago
  
  484d48ed
- Nextflow-ify bash command to extract median read length · 97e72a8b
  Gervaise Henry authored 4 years ago
  
  97e72a8b
- Nextflow-ify bash command to extract median read length · 172d3212
  Gervaise Henry authored 4 years ago
  
  172d3212