Commits · 9fbc23766c7cb70e77ba763df79531d17e8f1d0c · Mirrors / biopet.biopet

11 Jan, 2016 4 commits
- fix tiny setting · 9fbc2376
  Sander Bollen authored Jan 11, 2016
  
  9fbc2376
- Change gvcf input · 6ebf4f39
  Peter van 't Hof authored Jan 11, 2016
  
  6ebf4f39
- Merge bed records · 7bedb39b
  Peter van 't Hof authored Jan 11, 2016
  
  7bedb39b
- Improved logging · 798f296b
  Peter van 't Hof authored Jan 11, 2016
  
  798f296b
06 Jan, 2016 1 commit
- fix merge request issues · a161a802
  Sander Bollen authored Jan 06, 2016
  
  a161a802
05 Jan, 2016 2 commits
- merge bed file to prevent massive files · 29ddfee6
  Sander Bollen authored Jan 05, 2016
  
  29ddfee6
- manwe wrapper fixes · 7bea0e95
  Sander Bollen authored Jan 05, 2016
  
  7bea0e95
22 Dec, 2015 1 commit
- Fix issue #248 · 000db84e
  Peter van 't Hof authored Dec 22, 2015
  
  000db84e
18 Dec, 2015 4 commits
- Change back to get · 7e542a61
  Peter van 't Hof authored Dec 18, 2015
  
  7e542a61
- More fail safe · a6d7e825
  Peter van 't Hof authored Dec 18, 2015
  
  a6d7e825
- Simplify · 8d9d194b
  Peter van 't Hof authored Dec 18, 2015
  
  8d9d194b
- Fixed args · 182c68fa
  Peter van 't Hof authored Dec 18, 2015
  
  182c68fa
15 Dec, 2015 4 commits
- 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
- Fixed dir of samtools flagstat · 96c56bc1
  Peter van 't Hof authored Dec 15, 2015
  
  96c56bc1
- Fixed args · 6a4c600a
  Peter van 't Hof authored Dec 15, 2015
  
  6a4c600a
14 Dec, 2015 1 commit
- Fixed args for CollectGcBiasMetrics · 4e003490
  Peter van 't Hof authored Dec 14, 2015
  
  4e003490
11 Dec, 2015 4 commits
- Remove unused import · 59fa2049
  Peter van 't Hof authored Dec 11, 2015
  
  59fa2049
- Fixed typo · 1bf61988
  Peter van 't Hof authored Dec 11, 2015
  
  1bf61988
- Store adapter stats name in a single variable · 4945f3ce
  bow authored Dec 11, 2015
  
  4945f3ce
- Use correct copyright header for Cutadapt wrapper in Flexiprep · 9bdd6fdd
  bow authored Dec 11, 2015
  
  9bdd6fdd
10 Dec, 2015 4 commits
- Use file names for logging errors in Flexiprep Cutadapt wrapper instead of read names · 9d748545
  bow authored Dec 10, 2015
  
  9d748545
- Update None pattern match to use catch-all clause · d207b97f
  bow authored Dec 10, 2015
  
  d207b97f
- Update adapters summary stats to be Map[String, Any] instead of (String, Int) · c1ccaa97
  bow authored Dec 10, 2015
  
  c1ccaa97
- Initial fix for #238 · e7541377
  bow authored Dec 10, 2015
```
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.
```
  e7541377
03 Dec, 2015 5 commits
- Upgrade queue to 3.5 · a47decde
  Peter van 't Hof authored Dec 03, 2015
  
  a47decde
- Added plot · 27b892e6
  Peter van 't Hof authored Dec 03, 2015
  
  27b892e6
- Fixed report with regions · 8923196d
  Peter van 't Hof authored Dec 03, 2015
  
  8923196d
- Fixed wrong tag · 692208f2
  Peter van 't Hof authored Dec 03, 2015
  
  692208f2
- Style fixes · fe542841
  Peter van 't Hof authored Dec 03, 2015
  
  fe542841
30 Nov, 2015 1 commit
- Fixed vcf index files · 55629dcb
  Peter van 't Hof authored Nov 30, 2015
  
  55629dcb
29 Nov, 2015 4 commits
- Fix graph issues · d107727c
  Peter van 't Hof authored Nov 29, 2015
  
  d107727c
- Added index to vt jobs · 6cb4dcbe
  Peter van 't Hof authored Nov 29, 2015
  
  6cb4dcbe
- Style fix · 88d47fcf
  Peter van 't Hof authored Nov 29, 2015
  
  88d47fcf
- Fixed md5sums · 3f7a6044
  Peter van 't Hof authored Nov 29, 2015
  
  3f7a6044
27 Nov, 2015 4 commits
- Fix dict generate · 32692078
  Peter van 't Hof authored Nov 27, 2015
  
  32692078
- Check for bowtie2-Index files in bowtie2 · 5bc1ea8e
  Wai Yi Leung authored Nov 27, 2015
  
  5bc1ea8e
- Check for bowtie2-Index files in bowtie2 · e945e4db
  Wai Yi Leung authored Nov 27, 2015
  
  e945e4db
- Fix bcftools executeables · 339c0413
  Peter van 't Hof authored Nov 27, 2015
  
  339c0413
26 Nov, 2015 1 commit
- Fix vcf stats · 7aeda35f
  Peter van 't Hof authored Nov 26, 2015
  
  7aeda35f