Commits · 4b245b7df63011bf150f6a597661a17113efbfb2 · Holland Computing Center / chipathlon · GitLab

16 Mar, 2016 7 commits
- Fixed typo in _add_align. · 4b245b7d
  aknecht2 authored Mar 16, 2016
  
  4b245b7d
- Fixed workflow_job extension checking. Fixed bowtie2 extension checking. · 699d9178
  aknecht2 authored Mar 16, 2016
  
  699d9178
- Fixed typo in _add_align. Adjusted naming in _check_grch38. · 47fa3240
  aknecht2 authored Mar 16, 2016
  
  47fa3240
- Genome files now tracked in run_data for later use. · 265b2178
  aknecht2 authored Mar 16, 2016
  
  265b2178
- Cleaned up _check_grch38. Added handling for prefixes. · cd2a9aa4
  aknecht2 authored Mar 16, 2016
  
  cd2a9aa4
- Fixed _add_file in check_grch38. · 241c210e
  aknecht2 authored Mar 16, 2016
  
  241c210e
- Added generic _add_file function. · dfaec1ed
  aknecht2 authored Mar 16, 2016
  
  dfaec1ed
15 Mar, 2016 10 commits
- Add .'ing of Lmod init script · 474a5f59
  Adam Caprez authored Mar 15, 2016
```
Condor jobs do not see normal user shell init scripts.  Have to
explicitly dot it in for module to work.
```
  474a5f59
- Fix module name · 5e4d0e41
  Adam Caprez authored Mar 15, 2016
  
  5e4d0e41
- Fixed download function. · 48537682
  aknecht2 authored Mar 15, 2016
  
  48537682
- Revert "Updated download_fastq to use 4096b chunks." · a728e126
  aknecht2 authored Mar 15, 2016
```
This reverts commit 1c068ff3.
```
  a728e126
- Updated download_fastq to use 4096b chunks. · 1c068ff3
  aknecht2 authored Mar 15, 2016
  
  1c068ff3
- Update tester script for new classname, config file · ec3b6ada
  Adam Caprez authored Mar 15, 2016
  
  ec3b6ada
- Change to setuptools to preserve file execute perms · 37da6588
  Adam Caprez authored Mar 15, 2016
  
  37da6588
- Changed overwrite default to True. Adjusted download to the correct md5 value. · dc7c0b9c
  aknecht2 authored Mar 15, 2016
  
  dc7c0b9c
- Updated download util. Removed default username/password from tester. · 4d651c4d
  aknecht2 authored Mar 15, 2016
  
  4d651c4d
- Spell check 'argumnet'. · 70423587
  aknecht2 authored Mar 15, 2016
  
  70423587
14 Mar, 2016 23 commits
- Fix non-existant variable name · 09b3fda7
  Adam Caprez authored Mar 14, 2016
  
  09b3fda7
- Changes to handle genome files containing `.` chars · f1fcb137
  Adam Caprez authored Mar 14, 2016
  
  f1fcb137
- Add 2nd output file for bowtie2 quality info · 689f928d
  Adam Caprez authored Mar 14, 2016
  
  689f928d
- Add file extension entry for bowtie2 quality output · 5587ef2d
  Adam Caprez authored Mar 14, 2016
  
  5587ef2d
- Add stderr redirect to capture Bowtie2 quality info · 99df5c29
  Adam Caprez authored Mar 14, 2016
  
  99df5c29
- Removed unnecessary print statements. Correctly generate sites from config. · ceb12636
  aknecht2 authored Mar 14, 2016
  
  ceb12636
- Fixed PFN. · 3d2f093e
  aknecht2 authored Mar 14, 2016
  
  3d2f093e
- Added base_file adding to check_genome. · c7dc50af
  aknecht2 authored Mar 14, 2016
  
  c7dc50af
- Added dax debug. · a05847f0
  aknecht2 authored Mar 14, 2016
  
  a05847f0
- Updated config to a class variable. · 69f47ee0
  aknecht2 authored Mar 14, 2016
  
  69f47ee0
- Added config loading. · fee211b8
  aknecht2 authored Mar 14, 2016
  
  fee211b8
- Adjusted file iteration in workflow. · 266ffda9
  aknecht2 authored Mar 14, 2016
  
  266ffda9
- Added additional_inputs: null to samtools_sam_to_bam. · 6ff495c2
  aknecht2 authored Mar 14, 2016
  
  6ff495c2
- Fixed workflow_job validation. Adjust bwa_sai_to_sam, now has additional_inputs: null · 643c86fc
  aknecht2 authored Mar 14, 2016
  
  643c86fc
- Check for NoneType in module jobs. · d0e63648
  aknecht2 authored Mar 14, 2016
  
  d0e63648
- Fixed typo in workflow module. · 87b919bf
  aknecht2 authored Mar 14, 2016
  
  87b919bf
- Fixed workflow dependency loading. · 42e8e0a2
  aknecht2 authored Mar 14, 2016
  
  42e8e0a2
- Adjusted input file auto-detection. · 0c1af9dc
  aknecht2 authored Mar 14, 2016
  
  0c1af9dc
- Fixed input/output unpacking. · afaa15b9
  aknecht2 authored Mar 14, 2016
  
  afaa15b9
- Removed periods from grch38p6 genome. · 108f7394
  aknecht2 authored Mar 14, 2016
  
  108f7394
- Updated file extension handling in workflow_job. Added error handling to workflow_module. · b91288c9
  aknecht2 authored Mar 14, 2016
  
  b91288c9
- job only creates if successful now. · 60aa42ca
  aknecht2 authored Mar 14, 2016
  
  60aa42ca
- Added sai to file_extensions. Typo fixes for workflow_job & module. · 2a009c0c
  aknecht2 authored Mar 14, 2016
  
  2a009c0c