Commits · c28fcce24b0a7aa58cf4fbe5b1b59e835c5cb21d · GUDMAP_RBK / RNA-seq · GitLab

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Jan 19, 2021
- Fix fastq file error detection · c28fcce2
  Gervaise Henry authored 4 years ago
  
  c28fcce2
- Make dummy fastqc output if fail · 3b6afce4
  Gervaise Henry authored 4 years ago
  
  3b6afce4
- Detect malformed fastqs · f7559c64
  Gervaise Henry authored 4 years ago
  
  f7559c64
- Fix spike/species asignment for unexpected · 3b99da50
  Gervaise Henry authored 4 years ago
  
  3b99da50
- Fix python else syntac · 00b82094
  Gervaise Henry authored 4 years ago
  
  00b82094
- Further remove parsing restrictions from stranded/spike/species · 29e5ce6b
  Gervaise Henry authored 4 years ago
  
  29e5ce6b
- Remove ability to count fastqs manually from file.csv · f1d40472
  Gervaise Henry authored 4 years ago
  
  f1d40472
- Don't parse manual ends from file.csv anymore · 6b6268c3
  Gervaise Henry authored 4 years ago
  
  6b6268c3
- Fix elif · 2ef85c6b
  Gervaise Henry authored 4 years ago
  
  2ef85c6b
- Handle blank endness better · 41f6e91a
  Gervaise Henry authored 4 years ago
  
  41f6e91a
- Remove redundant check for multiple fastqs in parse metadata · 538a5074
  Gervaise Henry authored 4 years ago
  
  538a5074
- Allow .R[1,2] and _R[1,2] fastqs · 56d35250
  Gervaise Henry authored 4 years ago
  
  56d35250
- Filter input bag export config to only get fastq's matching convention · 5d9c691f
  Gervaise Henry authored 4 years ago
  
  5d9c691f
- Only used fastq's named correctly · d78689ad
  Gervaise Henry authored 4 years ago
  
  d78689ad
- Physically move fastqc process up · 51f9e8ff
  Gervaise Henry authored 4 years ago
  
  51f9e8ff
- Fix fastq run before trim · 7d4badfe
  Gervaise Henry authored 4 years ago
  
  7d4badfe
- Move fastqc before trim · 67b0e41e
  Gervaise Henry authored 4 years ago
  
  67b0e41e
- Allow unexpected values for stranded/spike/species · 8a91ad1b
  Gervaise Henry authored 4 years ago
  
  8a91ad1b
Jan 18, 2021
- Move mem param to sort · 527d9358
  Gervaise Henry authored 4 years ago
  
  527d9358
- Copy samtools mem param fix to align sample · 0bfa5ba9
  Gervaise Henry authored 4 years ago
  
  0bfa5ba9
- Double excape * · 4ed64765
  Gervaise Henry authored 4 years ago
  
  4ed64765
- Add -m to samtools sort · 5988eb64
  Gervaise Henry authored 4 years ago
  
  5988eb64
Jan 15, 2021
- Add in missinng process config. · fa009e23
  Venkat Malladi authored 4 years ago
  
  fa009e23
- Update biohpc.config · 73490420
  Venkat Malladi authored 4 years ago
  
  73490420
- Update aws.config · bce79412
  Venkat Malladi authored 4 years ago
  
  bce79412
- Fix process name in config file · a36cfc7b
  Venkat Malladi authored 4 years ago
  
  a36cfc7b
Jan 14, 2021
- Fix script name · effe7d20
  Gervaise Henry authored 4 years ago
  
  effe7d20
- Update manifest version · 165fc906
  Gervaise Henry authored 4 years ago
  
  165fc906
- Fix mistype error · f839e74f
  Gervaise Henry authored 4 years ago
  
  f839e74f
- Change replicate count for badges to count all replicates that match major version number · b104fc98
  Gervaise Henry authored 4 years ago
  
  b104fc98
- Output execution run rid to tracking for fail and failPre Execution · 413e1ce6
  Gervaise Henry authored 4 years ago
  
  413e1ce6
- Split failPreExecution into 2 processes · 982092fb
  Gervaise Henry authored 4 years ago
  
  982092fb
Jan 12, 2021
- Fix complete/fail date tracking passing · 71592755
  Gervaise Henry authored 4 years ago
  
  71592755
Jan 11, 2021
- Fix json uploads to tracking · 312a6047
  Gervaise Henry authored 4 years ago
  
  312a6047
- Fix date ouput for finalize execution run table · 0b6fa2aa
  Gervaise Henry authored 4 years ago
  
  0b6fa2aa
- Fix execution run rid upload to tracking table · 8b71fe3c
  Gervaise Henry authored 4 years ago
  
  8b71fe3c
- Pass whole json file to curl for lamda into AWS qc table · f8c2c290
  Gervaise Henry authored 4 years ago
  
  f8c2c290
- Add newlines to trackStart · f1f92c5b
  Gervaise Henry authored 4 years ago
  
  f1f92c5b
- Add execution run rid to tracking table · 99d29c0d
  Gervaise Henry authored 4 years ago
  
  99d29c0d
- Revert fail execution run · a93462f9
  Gervaise Henry authored 4 years ago
  
  a93462f9