Commits · efbc8c595271b335ef857a4b211faa2daac20981 · BICF / Astrocyte / cellranger_count

Mar 10, 2019
- Add/update CI with simple tests for kit v 2 and 3, ref v 1.2.0 and 3.0.0, cellranger v 2 and 3 · efbc8c59
  Gervaise Henry authored 6 years ago
  
  efbc8c59
- Update .gitignore with nextflow analysis folders in root · 8b8d2d1e
  Gervaise Henry authored 6 years ago
  
  8b8d2d1e
- Add nextflow.config to pipeline root folder · 76d6ec90
  Gervaise Henry authored 6 years ago
  
  76d6ec90
- Change kitVersion from numeric to string value · 9fc2b894
  Gervaise Henry authored 6 years ago
  
  9fc2b894
Mar 05, 2019
- Merge branch '11-10x.kit.version' into 'develop' · fd2352e2
  Gervaise Henry authored 6 years ago
```
Resolve "Add parameter for 10x kit version"

Closes #11

See merge request !12
```
  fd2352e2
- Add 10x chemistry version as option to address #11 · 735fdf18
  Gervaise Henry authored 6 years ago
  
  735fdf18
- Fix indent in .gitlab-ci.yml · e0ada3da
  Gervaise Henry authored 6 years ago
  
  e0ada3da
- Link design file from testdata for CI · 68345f57
  Gervaise Henry authored 6 years ago
  
  68345f57
- Merge branch '4-output.folder' into 'develop' · 6cb1be4d
  Gervaise Henry authored 6 years ago
```
Resolve "Create output directory option"

Closes #4

See merge request !11
```
  6cb1be4d
- Add cli parameter option for output folder to address #4 · 8fc88d18
  Gervaise Henry authored 6 years ago
  
  8fc88d18
Mar 04, 2019
- Update gitignore · 6905cdca
  Gervaise Henry authored 6 years ago
  
  6905cdca
- Merge branch '7-fix.config.mem' into 'develop' · 6d12da60
  Gervaise Henry authored 6 years ago
```
Resolve "Fix config file"

Closes #7

See merge request !10
```
  6d12da60
- Merge branch '2-ref.genome.folder' into 'develop' · 5db938dc
  Gervaise Henry authored 6 years ago
```
Resolve "Remove reference genome full folder"

Closes #2

See merge request !9
```
  5db938dc
- Make reference folder follow standard to fix #2 · 3d24ed7e
  Gervaise Henry authored 6 years ago
  
  3d24ed7e
- Add minimum memory for cellranger count to 120GB to fix #7 · 9b8ae1b3
  Gervaise Henry authored 6 years ago
  
  9b8ae1b3
- Merge branch '2-ref.genome.folder' into 'develop' · e944001c
  Gervaise Henry authored 6 years ago
```
Resolve "Remove reference genome full folder"

Closes #2

See merge request !8
```
  e944001c
- Remove the full folder for references to fix #2 · 8aac15b4
  Gervaise Henry authored 6 years ago
  
  8aac15b4
- Merge branch '9-cellranger_ref3.0.0' into 'develop' · 2c16bfba
  Gervaise Henry authored 6 years ago
```
Resolve "Add cellranger references version 3.0.0 as options"

Closes #9

See merge request !7
```
  2c16bfba
- Merge branch 'develop' into '9-cellranger_ref3.0.0' · 0408200d
  Gervaise Henry authored 6 years ago
```
Fix cellranger version variable type

See merge request !6
```
  0408200d
- Merge branch '8-cellranger3.0.2' into 'develop' · 89f02a93
  Gervaise Henry authored 6 years ago
```
Resolve "Add cellranger 3.0.2 as option"

Closes #8

See merge request !5
```
  89f02a93
- Change version variable to string to fix #8 · 517ccbe9
  Gervaise Henry authored 6 years ago
  
  517ccbe9
- Add reference version 3.0.0 to address #9 · b131fbed
  Gervaise Henry authored 6 years ago
  
  b131fbed
- Merge branch '8-cellranger3.0.2' into 'develop' · 0ecff9bd
  Gervaise Henry authored 6 years ago
```
Resolve "Add cellranger 3.0.2 as option"

Closes #8

See merge request !4
```
  0ecff9bd
- Add 3.0.2 as a param option in astrocyte-pkg.yml, main.nf and biohpc.config to address #8 · fd8f3ac6
  Gervaise Henry authored 6 years ago
  
  fd8f3ac6
Feb 07, 2019
- Merge branch '1-cellranger3.0.1' into 'develop' · 1a425310
  Gervaise Henry authored 6 years ago
```
Resolve "Add cellranger v3.0.1"

Closes #1

See merge request !3
```
  1a425310
- Add params.version to main.nf to complete #1 · 23282d4e
  Gervaise Henry authored 6 years ago
  
  23282d4e
- Merge branch '1-cellranger3.0.1' into 'develop' · c9486db9
  Gervaise Henry authored 6 years ago
```
Resolve "Add cellranger v3.0.1"

Closes #1

See merge request !2
```
  c9486db9
- Implement VM cellranger version handling for #1 · bea0bb6d
  Gervaise Henry authored 6 years ago
  
  bea0bb6d
- Merge branch 'develop' into '1-cellranger3.0.1' · 3806d914
  Gervaise Henry authored 6 years ago
```
Merge hotfix into branch

See merge request !1
```
  3806d914
- Fixes design file overwrite #6 · 58df1814
  Gervaise Henry authored 6 years ago
  
  58df1814
Sep 11, 2018
- Embed module load cellranger into if/then/else · a2733bff
  Gervaise Henry authored 6 years ago
  
  a2733bff
- Point transcriptome to ./ · 2fb61286
  Gervaise Henry authored 6 years ago
  
  2fb61286
Sep 07, 2018
- Fix designFile location passage to checkDesignFile process · 01a09551
  Gervaise Henry authored 6 years ago
  
  01a09551
- Hardwire ref genome locations into astrocyte yml · 2ada067d
  Gervaise Henry authored 6 years ago
  
  2ada067d
- Fix debug output for genomes · 5f3b547d
  Gervaise Henry authored 6 years ago
  
  5f3b547d
- Add more report for genome fail · ed43083f
  Gervaise Henry authored 6 years ago
  
  ed43083f
- Revert and add outputs for genome param and ref to error exit output · bf96062e
  Gervaise Henry authored 6 years ago
  
  bf96062e
- Revert genomes changes and try using {} · ee5e2fd6
  Gervaise Henry authored 6 years ago
  
  ee5e2fd6
Sep 05, 2018
- Update main.nf · b7c95b73
  Gervaise Henry authored 6 years ago
  
  b7c95b73
- Update main.nf · 30d514f5
  Gervaise Henry authored 6 years ago
  
  30d514f5