Commits · 2b37111032bbe762fbd90a6769ef7fbf5fa8b5c2 · BICF / Astrocyte / cellranger_mkfastq

31 Dec, 2019 6 commits
- Try to get aws to copy bcl.tar.gz properly into untar process with path instead of file · 2b371110
  Gervaise Henry authored Dec 31, 2019
  
  2b371110
- Merge branch '39-aws' into 'develop' · 942677d9
  Gervaise Henry authored Dec 31, 2019
```
39 aws

See merge request !57
```
  942677d9
- Fix simple2 ci · d1f74a99
  Gervaise Henry authored Dec 31, 2019
  
  d1f74a99
- Fix CI to use standard config (biohpc with cluster) · ba85c18a
  Gervaise Henry authored Dec 31, 2019
  
  ba85c18a
- Make ready for merge · fe8fef7f
  Gervaise Henry authored Dec 31, 2019
  
  fe8fef7f
- Squash many small commits to get working · 428d3688
  Gervaise Henry authored Dec 28, 2019
  
  428d3688
28 Dec, 2019 2 commits
- Add max timeout for aws to 1hr · 7ecda2fb
  Gervaise Henry authored Dec 28, 2019
  
  7ecda2fb
- Set scripts as inputs · 458eec97
  Gervaise Henry authored Dec 28, 2019
  
  458eec97
27 Dec, 2019 21 commits
- Remove singularity automount from biohpc config · 028dbf32
  Gervaise Henry authored Dec 27, 2019
  
  028dbf32
- Add default docker image to aws config · 057cedcd
  Gervaise Henry authored Dec 27, 2019
  
  057cedcd
- Remove unused precesses in aws configs · 2c877846
  Gervaise Henry authored Dec 27, 2019
  
  2c877846
- Update aws configs · f8a74a61
  Gervaise Henry authored Dec 27, 2019
  
  f8a74a61
- Temporarily remove pytests and multiqc artifact · ef176f42
  Gervaise Henry authored Dec 27, 2019
  
  ef176f42
- Remove cellranger ran fastqc output · 4ee9a681
  Gervaise Henry authored Dec 27, 2019
  
  4ee9a681
- Update mkfastq outputs · 2427f43a
  Gervaise Henry authored Dec 27, 2019
  
  2427f43a
- Remove SLURM options from mkfastq process · 6564fa23
  Gervaise Henry authored Dec 27, 2019
  
  6564fa23
- Remove conda env from process · d61b199d
  Gervaise Henry authored Dec 27, 2019
  
  d61b199d
- Remove logging from conda env in checkDesignFile to see if in base image · 1fac8db4
  Gervaise Henry authored Dec 27, 2019
  
  1fac8db4
- Try putting conda env to install packages into checkDesignFile · 0596edd0
  Gervaise Henry authored Dec 27, 2019
  
  0596edd0
- Temp remove version and multiqc processes · 121b371f
  Gervaise Henry authored Dec 27, 2019
  
  121b371f
- Version bump to bicfbase and python3 · 26bdc114
  Gervaise Henry authored Dec 27, 2019
  
  26bdc114
- Fix countDesign queue · 98a2e2cc
  Gervaise Henry authored Dec 27, 2019
  
  98a2e2cc
- Add singularity automount · 63a1f19a
  Gervaise Henry authored Dec 27, 2019
  
  63a1f19a
- Update biohpc.config · da54554d
  Gervaise Henry authored Dec 27, 2019
  
  da54554d
- Update biohpc.config · 9b8bab0c
  Gervaise Henry authored Dec 27, 2019
  
  9b8bab0c
- Change withLabel to withName in bicf.config · ce84bf75
  Gervaise Henry authored Dec 27, 2019
  
  ce84bf75
- Make bicfbase default container · 43d6de71
  Gervaise Henry authored Dec 27, 2019
  
  43d6de71
- Remove redudnant config · 419b8518
  Gervaise Henry authored Dec 27, 2019
  
  419b8518
- Move process containers to profile configs · 91f091b0
  Gervaise Henry authored Dec 27, 2019
  
  91f091b0
26 Dec, 2019 6 commits
- Fix bicfbase version · 6aeb351b
  Gervaise Henry authored Dec 26, 2019
  
  6aeb351b
- Remove modules and queues from nf · 27517310
  Gervaise Henry authored Dec 26, 2019
  
  27517310
- Add process config for countDesign · c9ee430e
  Gervaise Henry authored Dec 26, 2019
  
  c9ee430e
- Remove error in config · 8f669fe8
  Gervaise Henry authored Dec 26, 2019
  
  8f669fe8
- Add BioHPC profile to CI · e0069eaf
  Gervaise Henry authored Dec 26, 2019
  
  e0069eaf
- Add docker containers for most processes · 1536d759
  Gervaise Henry authored Dec 26, 2019
  
  1536d759
23 Dec, 2019 1 commit
- Update configs · 13f6ec3d
  Gervaise Henry authored Dec 23, 2019
  
  13f6ec3d
20 Dec, 2019 3 commits
- Update .gitlab-ci.yml · 83d88a4e
  Gervaise Henry authored Dec 20, 2019
  
  83d88a4e
- Remove concurrency test · 2cd079e6
  Gervaise Henry authored Dec 20, 2019
  
  2cd079e6
- Test concurrency fix · 1fd8b392
  Gervaise Henry authored Dec 20, 2019
  
  1fd8b392
08 Nov, 2019 1 commit
- Add cluster hold option in biohpc config · e0a75caf
  Gervaise Henry authored Nov 08, 2019
  
  e0a75caf