Commits · ecd4e76f3c90af4695cfa7292a22021c7937273a · GUDMAP_RBK / RNA-seq · GitLab

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Jan 26, 2021
- Add new py tests for integration and override · ecd4e76f
  Gervaise Henry authored 4 years ago
  
  ecd4e76f
- Fix new force var names · 57529bc9
  Gervaise Henry authored 4 years ago
  
  57529bc9
- Remove unnecessary excape · a3d8f200
  Gervaise Henry authored 4 years ago
  
  a3d8f200
- Add missing excapes · e7024f45
  Gervaise Henry authored 4 years ago
  
  e7024f45
- Fix qutes to echo · 4d50fe8f
  Gervaise Henry authored 4 years ago
  
  4d50fe8f
- Add qutes to echo · c03c60c9
  Gervaise Henry authored 4 years ago
  
  c03c60c9
- Add force params for stranded and spike · 59cb654a
  Gervaise Henry authored 4 years ago
  
  59cb654a
- Double excape slash · 0511ac1a
  Gervaise Henry authored 4 years ago
  
  0511ac1a
- Excape bash vars · b390a5e5
  Gervaise Henry authored 4 years ago
  
  b390a5e5
- Update create test data with new metadata model · 42785f19
  Gervaise Henry authored 4 years ago
  
  42785f19
- Update create test data with new metadata model · b5569b5b
  Gervaise Henry authored 4 years ago
  
  b5569b5b
- URLify hatrac location for outputBag · b15b2201
  Gervaise Henry authored 4 years ago
  
  b15b2201
- Fix getRef use of new spike values · ddc9ef20
  Gervaise Henry authored 4 years ago
  
  ddc9ef20
Jan 25, 2021
- Update parseMetadata ci test · c2a7f9b0
  Gervaise Henry authored 4 years ago
  
  c2a7f9b0
- Temporarily change CI integration tests to use dev server (staging doesn't have model changes) · c4c258bf
  Gervaise Henry authored 4 years ago
  
  c4c258bf
- Change logic for uploadOutputBag · a503d1e2
  Gervaise Henry authored 4 years ago
  
  a503d1e2
- Merge data error pre-Execution run · 77410b76
  Gervaise Henry authored 4 years ago
  
  77410b76
- Add blank mRNA_QC on data fail · f4e88555
  Gervaise Henry authored 4 years ago
  
  f4e88555
- Remove unnecessary RID output parsing · 03f13a82
  Gervaise Henry authored 4 years ago
  
  03f13a82
- Convert strandedness from yes/no to t/f · a19f61d1
  Gervaise Henry authored 4 years ago
  
  a19f61d1
- Convert strandedness from yes/no to t/f · b9798355
  Gervaise Henry authored 4 years ago
  
  b9798355
- Update Has_Strand_Specific_Information to Strandedness · 3b3b7891
  Gervaise Henry authored 4 years ago
  
  3b3b7891
- Update Sequencing_Type to Experiment_Type · a5aedff5
  Gervaise Henry authored 4 years ago
  
  a5aedff5
- Allow Single Read for backwards compatibility · ca8d3a9c
  Gervaise Henry authored 4 years ago
  
  ca8d3a9c
Jan 20, 2021
- Fix Single Read in CI · 52c66590
  Gervaise Henry authored 4 years ago
  
  52c66590
- Update changelog · 5011fa37
  Gervaise Henry authored 4 years ago
  
  5011fa37
- Change Single Read to Single End · 797354e0
  Gervaise Henry authored 4 years ago
  
  797354e0
- Update errors in readme · ef06aea5
  Gervaise Henry authored 4 years ago
  
  ef06aea5
- Merge branch '108-samtools.mem' into 'develop' · 474a1d3e
  Venkat Malladi authored 4 years ago
```
Resolve "samtools sort: couldn't allocate memory for bam_mem"

Closes #109, #108, #107, #106, and #105

See merge request !64
```
  474a1d3e
- Update DAG · e1d95064
  Gervaise Henry authored 4 years ago
  
  e1d95064
- Use 1 less process for samtools threading and limit memto 75% of available · 1fe7d8b3
  Gervaise Henry authored 4 years ago
  
  1fe7d8b3
- Make sampled align use > 32GB nodes on BioHPC · 9e121dac
  Gervaise Henry authored 4 years ago
  
  9e121dac
- Catch error if fastq file error grep · e7c65fea
  Gervaise Henry authored 4 years ago
  
  e7c65fea
- Fix fastqc error detection · 985cef31
  Gervaise Henry authored 4 years ago
  
  985cef31
- Add back ends manual to parse ci unit · c36fec03
  Gervaise Henry authored 4 years ago
  
  c36fec03
- Add back ends manual to ci unit for parse, but manual · ded8b61b
  Gervaise Henry authored 4 years ago
  
  ded8b61b
- Add unexpected meta and fastq structure error ci integration tests · f83a3d8c
  Gervaise Henry authored 4 years ago
  
  f83a3d8c
- Add excape to bracket in echo · e1819c40
  Gervaise Henry authored 4 years ago
  
  e1819c40
- Remove ends manual from parse metadata unit ci · 8f5efffa
  Gervaise Henry authored 4 years ago
  
  8f5efffa
- Add premature fail execution run upload with fastq file error · 94dac4ed
  Gervaise Henry authored 4 years ago
  
  94dac4ed