Commits · 3f1278c80a816c11d7b4ce9e6e3768d8c1ebe2e1 · BICF / Astrocyte / cellranger_mkfastq

26 Apr, 2019 1 commit
- Report fastqc's from multiple flowcells separate · 3f1278c8
  Gervaise Henry authored Apr 26, 2019
  
  3f1278c8
25 Apr, 2019 3 commits
- Split version file gen to separate process, run single version/multiqc process · d5ba8a06
  Gervaise Henry authored Apr 25, 2019
  
  d5ba8a06
- Run multiple mkfastq if multiple bcls · 42d035c6
  Gervaise Henry authored Apr 25, 2019
  
  42d035c6
- Get untar to run on multiple bcls · de4aab57
  Gervaise Henry authored Apr 25, 2019
  
  de4aab57
23 Apr, 2019 1 commit
- Get tagging of fastqc working · 2fc45b33
  Gervaise Henry authored Apr 23, 2019
  
  2fc45b33
22 Apr, 2019 4 commits
- Try to get qcs for multiple flowcells in different folders · 280c7abf
  Gervaise Henry authored Apr 22, 2019
  
  280c7abf
- Merge branch '14-move.multiqc.config' into 'develop' · ea26d49c
  Gervaise Henry authored Apr 22, 2019
```
Resolve "Change location of multiqc config and name"

Closes #14

See merge request !15
```
  ea26d49c
- Fix config folder · 4dd48f74
  Gervaise Henry authored Apr 22, 2019
  
  4dd48f74
- Move multiqc config · 8e7182f6
  Gervaise Henry authored Apr 22, 2019
  
  8e7182f6
12 Apr, 2019 8 commits
- Merge branch '12-move.software.report' into 'develop' · 30ca743a
  Gervaise Henry authored Apr 12, 2019
```
Resolve "Move software version report to the bottom"

Closes #12

See merge request !13
```
  30ca743a
- Put custom content at the bottom of the reports · 338bf053
  Gervaise Henry authored Apr 12, 2019
  
  338bf053
- Move software report to bottom · befd5bf5
  Gervaise Henry authored Apr 12, 2019
  
  befd5bf5
- Update astrocyte_pkg.yml · ed3d36bf
  Gervaise Henry authored Apr 12, 2019
  
  ed3d36bf
- Merge branch '9-split.multiqc' into 'develop' · 474455b0
  Gervaise Henry authored Apr 12, 2019
```
Resolve "Split multiqc fastqc by r1/r2/i1"

Closes #9

See merge request !11
```
  474455b0
- Split fastqc reports by I1,R1,R2 · 1811a23f
  Gervaise Henry authored Apr 12, 2019
  
  1811a23f
- Merge branch '11_fastqcoptimize' into 'develop' · 21c3f273
  Gervaise Henry authored Apr 12, 2019
```
11 fastqcoptimize

See merge request !10
```
  21c3f273
- Fix · 7255080d
  Gervaise Henry authored Apr 12, 2019
  
  7255080d
11 Apr, 2019 2 commits
- Removed redundant command. · 7a60cbd7
  Jonathan Gesell authored Apr 11, 2019
  
  7a60cbd7
- Updated fastqc for better multithreading, updated module lists. · 2f5a2b47
  Jonathan Gesell authored Apr 11, 2019
  
  2f5a2b47
10 Apr, 2019 5 commits
- Merge branch '7-documentation' into 'develop' · f448eb64
  Gervaise Henry authored Apr 10, 2019
```
Resolve "Update Documentation"

Closes #7

See merge request !7
```
  f448eb64
- Add qc's to docs · a4c203b0
  Gervaise Henry authored Apr 10, 2019
  
  a4c203b0
- Add back test_data dir · e90a2d17
  Gervaise Henry authored Apr 10, 2019
  
  e90a2d17
- Update docs · 862a479e
  Gervaise Henry authored Apr 10, 2019
  
  862a479e
- Merge branch '6-multiqc' into 'develop' · a896a72c
  Gervaise Henry authored Apr 10, 2019
```
Resolve "Add MultiQC"

See merge request !6
```
  a896a72c
09 Apr, 2019 2 commits
- Add run name param · 181c0f05
  Gervaise Henry authored Apr 09, 2019
  
  181c0f05
- Add process tags · 852500e6
  Gervaise Henry authored Apr 09, 2019
  
  852500e6
08 Apr, 2019 4 commits
- Rejigger process queues · 919ebd3d
  Gervaise Henry authored Apr 08, 2019
  
  919ebd3d
- Remove premature reference script and set fastq process to use super queue · 0ad4bb2a
  Gervaise Henry authored Apr 08, 2019
  
  0ad4bb2a
- Change report order · 00b66d4c
  Gervaise Henry authored Apr 08, 2019
  
  00b66d4c
- Add custom multiqc report yaml with software versions · 42e5fcf0
  Gervaise Henry authored Apr 08, 2019
  
  42e5fcf0
07 Apr, 2019 2 commits
- Improve input file import of fastqc process · 9fe4abf2
  Gervaise Henry authored Apr 07, 2019
  
  9fe4abf2
- Add fastqc (needs input file optimization) · 7b474afc
  Gervaise Henry authored Apr 07, 2019
  
  7b474afc
05 Apr, 2019 2 commits
- Add basic multiqc process · 6e722372
  Gervaise Henry authored Apr 05, 2019
  
  6e722372
- Update astrocyte_pkg.yml to accept .tar or .tar.gz · c6bfd08e
  Gervaise Henry authored Apr 05, 2019
  
  c6bfd08e
04 Apr, 2019 1 commit
- Updated and corrected for Astrocyte · aef86ad7
  Jonathan Gesell authored Apr 04, 2019
  
  aef86ad7
28 Mar, 2019 2 commits
- Merge branch '2-optimize_makefastq' into 'develop' · 6e9d50a2
  Gervaise Henry authored Mar 28, 2019
```
# Conflicts:
#   workflow/main.nf
```
  6e9d50a2
- Added better multithredding utilization to Cellranger step. · eb4dd6b6
  Jonathan Gesell authored Mar 28, 2019
  
  eb4dd6b6
24 Mar, 2019 3 commits
- Merge branch '1-update' into 'develop' · 4e731fe0
  Gervaise Henry authored Mar 24, 2019
```
Resolve "Migrate cellranger_count basics"

See merge request !2
```
  4e731fe0
- Update README.md · 5dfa2268
  Gervaise Henry authored Mar 24, 2019
  
  5dfa2268
- Add astrocyte module load to CI · 5076c9d0
  Gervaise Henry authored Mar 24, 2019
  
  5076c9d0