Commits · 3c5e4e884ed9fc67145ef9d1424eb93a42221c8f · Mirrors / biopet.biopet

23 Dec, 2015 3 commits
- Added a prettyXmlPrinter · 3c5e4e88
  Peter van 't Hof authored Dec 23, 2015
  
  3c5e4e88
- Added sorting for samples · 2b882e6f
  Peter van 't Hof authored Dec 23, 2015
  
  2b882e6f
- Added function to convert kraken to krona output · 55b5629d
  Peter van 't Hof authored Dec 23, 2015
  
  55b5629d
18 Dec, 2015 7 commits
- Added tool for merging otu maps · 0b1fec3f
  Peter van 't Hof authored Dec 18, 2015
  
  0b1fec3f
- Added properties for debuging · d6694b38
  Peter van 't Hof authored Dec 18, 2015
  
  d6694b38
- Add settings · 86e7d090
  Peter van 't Hof authored Dec 18, 2015
  
  86e7d090
- Fixed double flexiprep · 8acebe9a
  Peter van 't Hof authored Dec 18, 2015
  
  8acebe9a
- Remove unneeded if statement · d7984e09
  Peter van 't Hof authored Dec 18, 2015
  
  d7984e09
- Fixed sample and lib id for flexiprep · 5aa027a2
  Peter van 't Hof authored Dec 18, 2015
  
  5aa027a2
- Fix sample IDs · 67db8906
  Peter van 't Hof authored Dec 18, 2015
  
  67db8906
17 Dec, 2015 11 commits
- Style fixes · 43100197
  Peter van 't Hof authored Dec 17, 2015
  
  43100197
- Switch to sample based analysis · 08070144
  Peter van 't Hof authored Dec 17, 2015
  
  08070144
- Fixed wrong job · c5669b7b
  Peter van 't Hof authored Dec 17, 2015
  
  c5669b7b
- Removed unused import · 6e2abf91
  Peter van 't Hof authored Dec 17, 2015
  
  6e2abf91
- Raise memory · 16e4e0cb
  Peter van 't Hof authored Dec 17, 2015
  
  16e4e0cb
- Adding todo's · 7e27eee9
  Peter van 't Hof authored Dec 17, 2015
  
  7e27eee9
- Added merge of otu tables and maps · 83c0d1ee
  Peter van 't Hof authored Dec 17, 2015
  
  83c0d1ee
- Expose subpipelines · 0a25827e
  Peter van 't Hof authored Dec 17, 2015
  
  0a25827e
- Added output files · 9c1384fb
  Peter van 't Hof authored Dec 17, 2015
  
  9c1384fb
- Added output files · f430f58c
  Peter van 't Hof authored Dec 17, 2015
  
  f430f58c
- Added extension for merge otu maps · 6f21013e
  Peter van 't Hof authored Dec 17, 2015
  
  6f21013e
16 Dec, 2015 13 commits
- Added extension for merge otu tables · 9698cb6d
  Peter van 't Hof authored Dec 16, 2015
  
  9698cb6d
- Raise default memory · e910b28a
  Peter van 't Hof authored Dec 16, 2015
  
  e910b28a
- Always use -f · 8fd9b095
  Peter van 't Hof authored Dec 16, 2015
  
  8fd9b095
- Style changes · a952ee2a
  Peter van 't Hof authored Dec 16, 2015
  
  a952ee2a
- Fixed outputdir · 4e8e65b2
  Peter van 't Hof authored Dec 16, 2015
  
  4e8e65b2
- Removed unused import · 09ec3169
  Peter van 't Hof authored Dec 16, 2015
  
  09ec3169
- Simplify modules · af8d9361
  Peter van 't Hof authored Dec 16, 2015
  
  af8d9361
- Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime · 5c344be9
  Peter van 't Hof authored Dec 16, 2015
  
  5c344be9
- Added closed reference method · c6a89d92
  Peter van 't Hof authored Dec 16, 2015
  
  c6a89d92
- Added extension for clased reference otu picking · 15cd85a4
  Peter van 't Hof authored Dec 16, 2015
  
  15cd85a4
- Adding output files · d222ab7e
  Peter van 't Hof authored Dec 16, 2015
  
  d222ab7e
- Added extension for flash · 0a00efdc
  Peter van 't Hof authored Dec 16, 2015
  
  0a00efdc
- Change default regexes · 283d34e3
  Peter van 't Hof authored Dec 16, 2015
  
  283d34e3
15 Dec, 2015 6 commits
- Merge branch 'fix-238' into 'develop' · 63c6517c
  Peter van 't Hof authored Dec 15, 2015
```
Fix for #238

The issue is caused by the Cutadapt summary not being aware of the
clipped sequence names. This merge request extends the existing Cutadapt
wrapper in the Flexiprep module and makes it so that the wrapper is
aware of FastQC.

See merge request !288
```
  63c6517c
- Merge remote-tracking branch 'remotes/origin/develop' into fix-238 · a482f22f
  Peter van 't Hof authored Dec 15, 2015
  
  a482f22f
- Merge branch 'fix-bammetrics_summary_switchup' into 'develop' · ac389d5d
  Peter van 't Hof authored Dec 15, 2015
```
Fix wrong metrics addition in BamMetrics

The CollectHsMetrics was incorrectly added as the CollectTargetedPcrMetrics. This commit fixes it.

See merge request !291
```
  ac389d5d
- Fix wrong metrics addition in BamMetrics · ca59e8ef
  bow authored Dec 15, 2015
```
The CollectHsMetrics was incorrectly added as the
CollectTargetedPcrMetrics. This commit fixes it.
```
  ca59e8ef
- Refactor match statements · 6c3170cc
  Peter van 't Hof authored Dec 15, 2015
  
  6c3170cc
- Merge branch 'fix-CollectGcBiasMetrics' into 'develop' · 02db36c5
  bow authored Dec 15, 2015
```
Fixed args for CollectGcBiasMetrics



See merge request !290
```
  02db36c5