Develop (!65) · Merge requests · GUDMAP_RBK / RNA-seq · GitLab

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develop into master

Merged Gervaise Henry requested to merge develop into master 4 years ago

Jan 20, 2021
- 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
- Fix no fastq error detail · 957b7679
  Gervaise Henry authored 4 years ago
  
  957b7679
- Fix no fastq's present in inputBag · f453a4e3
  Gervaise Henry authored 4 years ago
  
  f453a4e3
- Upgrade version to v1.0.3 · 6cdde011
  Gervaise Henry authored 4 years ago
  
  6cdde011
- Fix file structure error detection · b95cdee7
  Gervaise Henry authored 4 years ago
  
  b95cdee7
Jan 19, 2021
- Fix if then · 9c9d4191
  Gervaise Henry authored 4 years ago
  
  9c9d4191
- Fix endsManual assignment · 2464b2cb
  Gervaise Henry authored 4 years ago
  
  2464b2cb
- 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
- Update changelog · 1f07208d
  Gervaise Henry authored 4 years ago
  
  1f07208d
- Allow unexpected values for stranded/spike/species · 8a91ad1b
  Gervaise Henry authored 4 years ago
  
  8a91ad1b
- Update changelog · f4d642f5
  Gervaise Henry authored 4 years ago
  
  f4d642f5
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