Commits · fa11871a5efbc5211f8366743369876763241242 · GUDMAP_RBK / RNA-seq

Aug 05, 2020
- 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
- Nextflow-ify bash command to extract median read length · 38d411ee
  Gervaise Henry authored 4 years ago
  
  38d411ee
- Measure median trimmed read length and display in multiqc table report · d0be69da
  Gervaise Henry authored 4 years ago
  
  d0be69da
- Move read length num to str to python script · bfaf76ce
  Gervaise Henry authored 4 years ago
  
  bfaf76ce
- Convert num read length to str in bash · b949a3b0
  Gervaise Henry authored 4 years ago
  
  b949a3b0
- Extract read length from submitter metadata · e8b92b99
  Gervaise Henry authored 4 years ago
  
  e8b92b99
Jul 30, 2020
- Add back trackStart process · d691c1cf
  Gervaise Henry authored 4 years ago
  
  d691c1cf
Jul 23, 2020
- AWS Batch works · 9fe16dfb
  Gervaise Henry authored 4 years ago
  
  9fe16dfb
Jul 14, 2020
- Reformat runtime info · 3ab2e9b3
  Gervaise Henry authored 4 years ago
  
  3ab2e9b3
- Add pipeline version var to track · 113f2b7c
  Gervaise Henry authored 4 years ago
  
  113f2b7c
- Fix param reference in runtime info · 7f7e0e9d
  Gervaise Henry authored 4 years ago
  
  7f7e0e9d
- Add runtime info · 92edc38f
  Gervaise Henry authored 4 years ago
  
  92edc38f
May 13, 2020
- Stage experiment settings as ExperimentSettings.csv to prevent bash error · ea8a2c38
  Gervaise Henry authored 4 years ago
  
  ea8a2c38
May 11, 2020
- Add source param for getBag #50 · a36c189e
  Gervaise Henry authored 4 years ago
  
  a36c189e
May 05, 2020
- Change to staging.gudmap.org · ebab7cd7
  Gervaise Henry authored 4 years ago
  
  ebab7cd7
May 02, 2020
- Fix getData · 5e322c79
  Gervaise Henry authored 4 years ago
  
  5e322c79
- Fix multiqc output · ae564dba
  Gervaise Henry authored 4 years ago
  
  ae564dba
- Harmonize outputs, add multiqc output · 28cbd1f8
  Gervaise Henry authored 4 years ago
  
  28cbd1f8
- Harmonize logs · 85392b62
  Gervaise Henry authored 4 years ago
  
  85392b62
- Harmonize process logs (remove excess) · 558e7e78
  Gervaise Henry authored 4 years ago
  
  558e7e78
- Harmonize process comments · 76bc47cd
  Gervaise Henry authored 4 years ago
  
  76bc47cd
- Harmonize in script comments · 81a24580
  Gervaise Henry authored 4 years ago
  
  81a24580
- Fix featureCounts · a37b535c
  Gervaise Henry authored 4 years ago
  
  a37b535c