v0.0.1 (!37) · Merge requests · GUDMAP_RBK / RNA-seq · GitLab

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Merged v0.0.1

develop into master

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

Aug 11, 2020
- Version to 0.0.1 · 8a8ce097
  Gervaise Henry authored 4 years ago
  
  8a8ce097
Aug 10, 2020
- Merge branch 'new.qc.out' into 'develop' · fe51a743
  Venkat Malladi authored 4 years ago
```
Metadata output update

Closes #56 and #52

See merge request !36
```
  fe51a743
- Convert string to int for range checking in consistency test · 6341ca53
  Gervaise Henry authored 4 years ago
  
  6341ca53
- Change consistence test from exact match to within 1/100,000 change from expected · ade9acec
  Gervaise Henry authored 4 years ago
  
  ade9acec
- Update dag · 506a006b
  Gervaise Henry authored 4 years ago
  
  506a006b
- Convert gene symbols to EntrezID in count/tpm table · c41b4788
  Gervaise Henry authored 4 years ago
  
  c41b4788
Aug 08, 2020
- Add instructions for running from study RID · c99ba0ab
  Gervaise Henry authored 4 years ago
  
  c99ba0ab
- Add scripts to run from study RID · 158a687e
  Gervaise Henry authored 4 years ago
  
  158a687e
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
- Remove number formats from multiqc config · 72e1e94b
  Gervaise Henry authored 4 years ago
  
  72e1e94b
- 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
- Fix countData unit summary file name · a9b7c868
  Gervaise Henry authored 4 years ago
  
  a9b7c868
- 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
- Round median TIN to 2 dp · 740d2eff
  Gervaise Henry authored 4 years ago
  
  740d2eff
- 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 median TIN output · 079a7f6c
  Gervaise Henry authored 4 years ago
  
  079a7f6c
- 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
- Fix parseMetadata unit test · 67d6d8f4
  Gervaise Henry authored 4 years ago
  
  67d6d8f4
- 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
- Output read length as str · 42b5b070
  Gervaise Henry authored 4 years ago
  
  42b5b070
- Extract read length from submitter metadata · e8b92b99
  Gervaise Henry authored 4 years ago
  
  e8b92b99
Jul 31, 2020
- Merge branch 'ci' into 'develop' · 0b6630da
  Gervaise Henry authored 4 years ago
```
Ci

Closes #54, #48, and #27

See merge request !35
```
  0b6630da
- Fix consistency module #27 · 4539dba1
  Gervaise Henry authored 4 years ago
  
  4539dba1
- Move expected assigned into ci.yml #27 · b247d7e4
  Gervaise Henry authored 4 years ago
  
  b247d7e4
- Add consistency tests #27 · 3f55fde3
  Gervaise Henry authored 4 years ago
  
  3f55fde3
- Add -q nextflow flag in ci to test (needs to run code after nextflow) · a0c9fde5
  Gervaise Henry authored 4 years ago
  
  a0c9fde5
- Remove -bg nextflow flag in ci to test · b272565d
  Gervaise Henry authored 4 years ago
  
  b272565d
Jul 30, 2020
- Remove cache dependencies #27 · e76f7aff
  Gervaise Henry authored 4 years ago
  
  e76f7aff
- Fix cache dependencies #27 · b1e53c7d
  Gervaise Henry authored 4 years ago
  
  b1e53c7d
- Setup dummy se conssistency test with cache dependencies · ecc08451
  Gervaise Henry authored 4 years ago
  
  ecc08451
- Add qc outputs from integration tests for consistency tests #27 · 33fd5b4c
  Gervaise Henry authored 4 years ago
  
  33fd5b4c
- Test for pytest for parseMetadata: remove unnecessary print #54 · d7b38e88
  Gervaise Henry authored 4 years ago
  
  d7b38e88
- Test for pytest for parseMetadata: pass+fail test worked... #54 · ea7ca4ad
  Gervaise Henry authored 4 years ago
  
  ea7ca4ad
- Test for pytest for parseMetadata: supposed to fail #54 · f57f9950
  Gervaise Henry authored 4 years ago
  
  f57f9950
- Test for pytest for parseMetadata: supposed to pass #54 · 6fe96e00
  Gervaise Henry authored 4 years ago
  
  6fe96e00
- Test for pytest for parseMetadata: supposed to pass #54 · 22fbaf52
  Gervaise Henry authored 4 years ago
  
  22fbaf52
- Test for pytest for parseMetadata: force pass #54 · 729ee825
  Gervaise Henry authored 4 years ago
  
  729ee825
- Test for pytest for parseMetadata: force pass #54 · 50df04d1
  Gervaise Henry authored 4 years ago
  
  50df04d1
- Test for pytest for parseMetadata: supposed to pass #54 · 32f281b4
  Gervaise Henry authored 4 years ago
  
  32f281b4
- Test for pytest for parseMetadata: supposed to pass #54 · 7179e4ed
  Gervaise Henry authored 4 years ago
  
  7179e4ed
- Edit dataQC pytest: should fail #48 · e8780f74
  Gervaise Henry authored 4 years ago
  
  e8780f74
- Edit dataQC pytest: should pass #48 · 979e6af4
  Gervaise Henry authored 4 years ago
  
  979e6af4
- Test for pytest for parseMetadata: supposed to pass #54 · 042e9177
  Gervaise Henry authored 4 years ago
  
  042e9177
- Print output of parseMetadata pytest read · fe544976
  Gervaise Henry authored 4 years ago
  
  fe544976
- Print output of parseMetadata pytest read · 95aa209b
  Gervaise Henry authored 4 years ago
  
  95aa209b
- Test for pytest for parseMetadata: supposed to pass #54 · 58415f1c
  Gervaise Henry authored 4 years ago
  
  58415f1c
- Test for pytest for parseMetadata: supposed to pass #54 · dbb02aae
  Gervaise Henry authored 4 years ago
  
  dbb02aae
- Test for pytest for parseMetadata: supposed to pass #54 · 390a9b5d
  Gervaise Henry authored 4 years ago
  
  390a9b5d
- Test for pytest for parseMetadata: supposed to pass #54 · e4b4d6f5
  Gervaise Henry authored 4 years ago
  
  e4b4d6f5
- Test for pytest for parseMetadata: supposed to pass #54 · b7cceb94
  Gervaise Henry authored 4 years ago
  
  b7cceb94
- Test for pytest for parseMetadata: supposed to pass #54 · 0ab26d0d
  Gervaise Henry authored 4 years ago
  
  0ab26d0d
- Fail test for pytest for parseMetadata passed, test pass #54 · 2630f906
  Gervaise Henry authored 4 years ago
  
  2630f906
- Fix pytest for parseMetadata: expect fail #54 · eddf3c14
  Gervaise Henry authored 4 years ago
  
  eddf3c14
- Add pytest for parseMetadata: expect fail #54 · 5c4e2529
  Gervaise Henry authored 4 years ago
  
  5c4e2529
- Fix dataQC unit test: addition worked #48 · b702f897
  Gervaise Henry authored 4 years ago
  
  b702f897
- Test unit test addition for #48 · 419fa8c6
  Gervaise Henry authored 4 years ago
  
  419fa8c6
- Add initial trial for dataQC unit improvement #48 · 6ed76f56
  Gervaise Henry authored 4 years ago
  
  6ed76f56
- Merge branch 'aws.batch' into 'develop' · fa5e0d39
  Venkat Malladi authored 4 years ago
```
aws.batch

See merge request !34
```
  fa5e0d39
- Add back trackStart process · d691c1cf
  Gervaise Henry authored 4 years ago
  
  d691c1cf
- Update merge request template · 79306a34
  Gervaise Henry authored 4 years ago
  
  79306a34
- Update dag · 7946823f
  Gervaise Henry authored 4 years ago
  
  7946823f
- Add fastqc commad to unit now that using singularity run · 2c60afce
  Gervaise Henry authored 4 years ago
  
  2c60afce
- Revert fastq unit to singularity run · a70781aa
  Gervaise Henry authored 4 years ago
  
  a70781aa
- Try singularity exec for fastqc unit test · 24284602
  Gervaise Henry authored 4 years ago
  
  24284602
- Add new docker images to CI · d6f6fd25
  Gervaise Henry authored 4 years ago
  
  d6f6fd25
Jul 23, 2020
- Update README.md · 0dbc77e0
  Gervaise Henry authored 4 years ago
  
  0dbc77e0
- AWS Batch works · 9fe16dfb
  Gervaise Henry authored 4 years ago
  
  9fe16dfb
Jul 15, 2020
- Merge branch '10-process.aggregateQC' into 'develop' · 54da2992
  Venkat Malladi authored 4 years ago
```
Resolve "process_qc"

Closes #10

See merge request !33
```
  54da2992
- Move createTestData to test_data · 460d9e53
  Gervaise Henry authored 4 years ago
  
  460d9e53
Jul 14, 2020
- Update docs/dag.png · 59ed6f05
  Gervaise Henry authored 4 years ago
  
  59ed6f05
- Update README.md · f3e1ea29
  Gervaise Henry authored 4 years ago
  
  f3e1ea29
- Return background run to integratiion · 8d3d9dea
  Gervaise Henry authored 4 years ago
  
  8d3d9dea
- Reformat runtime info · 3ab2e9b3
  Gervaise Henry authored 4 years ago
  
  3ab2e9b3
- Remove nextflow -bg from integration test · 299899f4
  Gervaise Henry authored 4 years ago
  
  299899f4
- Add pipeline version var to track · 113f2b7c
  Gervaise Henry authored 4 years ago
  
  113f2b7c
- Update nextflow and singularity versions in CI · 98cf06b5
  Gervaise Henry authored 4 years ago
  
  98cf06b5
- Fix param reference in runtime info · 7f7e0e9d
  Gervaise Henry authored 4 years ago
  
  7f7e0e9d