Commits · d1f74a991f6b233d8f09761a5d54cbac262f2a9f · BICF / Astrocyte / cellranger_mkfastq

Dec 31, 2019
- Make ready for merge · fe8fef7f
  Gervaise Henry authored 5 years ago
  
  fe8fef7f
- Squash many small commits to get working · 428d3688
  Gervaise Henry authored 5 years ago
  
  428d3688
Dec 28, 2019
- Add max timeout for aws to 1hr · 7ecda2fb
  Gervaise Henry authored 5 years ago
  
  7ecda2fb
- Set scripts as inputs · 458eec97
  Gervaise Henry authored 5 years ago
  
  458eec97
Dec 27, 2019
- Remove singularity automount from biohpc config · 028dbf32
  Gervaise Henry authored 5 years ago
  
  028dbf32
- Add default docker image to aws config · 057cedcd
  Gervaise Henry authored 5 years ago
  
  057cedcd
- Remove unused precesses in aws configs · 2c877846
  Gervaise Henry authored 5 years ago
  
  2c877846
- Update aws configs · f8a74a61
  Gervaise Henry authored 5 years ago
  
  f8a74a61
- Remove cellranger ran fastqc output · 4ee9a681
  Gervaise Henry authored 5 years ago
  
  4ee9a681
- Update mkfastq outputs · 2427f43a
  Gervaise Henry authored 5 years ago
  
  2427f43a
- Remove SLURM options from mkfastq process · 6564fa23
  Gervaise Henry authored 5 years ago
  
  6564fa23
- Remove conda env from process · d61b199d
  Gervaise Henry authored 5 years ago
  
  d61b199d
- Remove logging from conda env in checkDesignFile to see if in base image · 1fac8db4
  Gervaise Henry authored 5 years ago
  
  1fac8db4
- Try putting conda env to install packages into checkDesignFile · 0596edd0
  Gervaise Henry authored 5 years ago
  
  0596edd0
- Temp remove version and multiqc processes · 121b371f
  Gervaise Henry authored 5 years ago
  
  121b371f
- Version bump to bicfbase and python3 · 26bdc114
  Gervaise Henry authored 5 years ago
  
  26bdc114
- Fix countDesign queue · 98a2e2cc
  Gervaise Henry authored 5 years ago
  
  98a2e2cc
- Add singularity automount · 63a1f19a
  Gervaise Henry authored 5 years ago
  
  63a1f19a
- Update biohpc.config · da54554d
  Gervaise Henry authored 5 years ago
  
  da54554d
- Update biohpc.config · 9b8bab0c
  Gervaise Henry authored 5 years ago
  
  9b8bab0c
- Change withLabel to withName in bicf.config · ce84bf75
  Gervaise Henry authored 5 years ago
  
  ce84bf75
- Make bicfbase default container · 43d6de71
  Gervaise Henry authored 5 years ago
  
  43d6de71
- Move process containers to profile configs · 91f091b0
  Gervaise Henry authored 5 years ago
  
  91f091b0
Dec 26, 2019
- Fix bicfbase version · 6aeb351b
  Gervaise Henry authored 5 years ago
  
  6aeb351b
- Remove modules and queues from nf · 27517310
  Gervaise Henry authored 5 years ago
  
  27517310
- Add process config for countDesign · c9ee430e
  Gervaise Henry authored 5 years ago
  
  c9ee430e
- Remove error in config · 8f669fe8
  Gervaise Henry authored 5 years ago
  
  8f669fe8
- Add docker containers for most processes · 1536d759
  Gervaise Henry authored 5 years ago
  
  1536d759
Dec 23, 2019
- Update configs · 13f6ec3d
  Gervaise Henry authored 5 years ago
  
  13f6ec3d
Nov 08, 2019
- Add cluster hold option in biohpc config · e0a75caf
  Gervaise Henry authored 5 years ago
  
  e0a75caf
Nov 07, 2019
- Remove depreciated file output unit tests · fd62f1c7
  Gervaise Henry authored 5 years ago
  
  fd62f1c7
- Remove publish dirs for intermediate processes · ffe94839
  Gervaise Henry authored 5 years ago
  
  ffe94839
- Fix #34 to remove trailing and leading whitespace in design file contents · c43e5767
  Jeremy Mathews authored 5 years ago
  
  c43e5767
Oct 01, 2019
- Add ghenry token for Nextflow Tower to biohpc.config and update Nextflow... · 1eb5757e
  Gervaise Henry authored 5 years ago
```
Add ghenry token for Nextflow Tower to biohpc.config and update Nextflow version (and include tower) in CI
```
  1eb5757e
Sep 10, 2019
- Corrected counter for file depth · a5f5444b
  Jonathan Gesell authored 5 years ago
  
  a5f5444b
- Added check for tar directory existance, and untarring of only that directory · c517ff78
  Jonathan Gesell authored 5 years ago
  
  c517ff78
Aug 29, 2019
- Remove spaces from design file · 68be71c4
  Jeremy Mathews authored 5 years ago
  
  68be71c4
Aug 14, 2019

Update main.nf · 9894e341
Gervaise Henry authored 5 years ago

9894e341

Update workflow/scripts/generate_references.py,... · a7adaad5

Gervaise Henry authored 5 years ago

Update workflow/scripts/generate_references.py, workflow/scripts/generate_versions.py, workflow/scripts/versions_fastqc.sh, workflow/tests/test_check_design.py, workflow/scripts/countDesign.sh, workflow/tests/test_fastqc.py, workflow/tests/test_mkfastq.py, workflow/tests/test_multiqc.py, workflow/tests/test_untarBCL.py, workflow/tests/test_versions.py, workflow/scripts/versions_mkfastq.sh, workflow/scripts/untarBCL.sh, workflow/scripts/check_design.py files

a7adaad5

Update check_design.py · e5695307
Gervaise Henry authored 5 years ago

e5695307