Commits · 10d0ce962963d53d90a2f2b749bec16ff3b437b3 · Mirrors / biopet.biopet

Dec 21, 2015
- Adding merge strategies · 10d0ce96
  Peter van 't Hof authored 9 years ago
  
  10d0ce96
- Added pipeline to executable · 60615f7d
  Peter van 't Hof authored 9 years ago
  
  60615f7d
Dec 18, 2015
- Init setup for multisample mapping pipeline · a416a47b
  Peter van 't Hof authored 9 years ago
  
  a416a47b
- Change back to get · 7e542a61
  Peter van 't Hof authored 9 years ago
  
  7e542a61
- More fail safe · a6d7e825
  Peter van 't Hof authored 9 years ago
  
  a6d7e825
- Simplify · 8d9d194b
  Peter van 't Hof authored 9 years ago
  
  8d9d194b
- Fixed args · 182c68fa
  Peter van 't Hof authored 9 years ago
  
  182c68fa
Dec 15, 2015
- Fix wrong metrics addition in BamMetrics · ca59e8ef
  bow authored 9 years ago
  
  The CollectHsMetrics was incorrectly added as the CollectTargetedPcrMetrics. This commit fixes it.
  ca59e8ef
- Refactor match statements · 6c3170cc
  Peter van 't Hof authored 9 years ago
  
  6c3170cc
- Fixed dir of samtools flagstat · 96c56bc1
  Peter van 't Hof authored 9 years ago
  
  96c56bc1
- Fixed args · 6a4c600a
  Peter van 't Hof authored 9 years ago
  
  6a4c600a
Dec 14, 2015
- Fixed args for CollectGcBiasMetrics · 4e003490
  Peter van 't Hof authored 9 years ago
  
  4e003490
Dec 11, 2015
- Remove unused import · 59fa2049
  Peter van 't Hof authored 9 years ago
  
  59fa2049
- Fixed typo · 1bf61988
  Peter van 't Hof authored 9 years ago
  
  1bf61988
- Store adapter stats name in a single variable · 4945f3ce
  bow authored 9 years ago
  
  4945f3ce
- Use correct copyright header for Cutadapt wrapper in Flexiprep · 9bdd6fdd
  bow authored 9 years ago
  
  9bdd6fdd
Dec 10, 2015
- Use file names for logging errors in Flexiprep Cutadapt wrapper instead of read names · 9d748545
  bow authored 9 years ago
  
  9d748545
- Update None pattern match to use catch-all clause · d207b97f
  bow authored 9 years ago
  
  d207b97f
- Update adapters summary stats to be Map[String, Any] instead of (String, Int) · c1ccaa97
  bow authored 9 years ago
  
  c1ccaa97
- Initial fix for #238 · e7541377
  bow authored 9 years ago
  
  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
Dec 03, 2015
- Upgrade queue to 3.5 · a47decde
  Peter van 't Hof authored 9 years ago
  
  a47decde
- Added plot · 27b892e6
  Peter van 't Hof authored 9 years ago
  
  27b892e6
- Fixed report with regions · 8923196d
  Peter van 't Hof authored 9 years ago
  
  8923196d
- Fixed wrong tag · 692208f2
  Peter van 't Hof authored 9 years ago
  
  692208f2
- Style fixes · fe542841
  Peter van 't Hof authored 9 years ago
  
  fe542841
Nov 30, 2015
- Fixed vcf index files · 55629dcb
  Peter van 't Hof authored 9 years ago
  
  55629dcb
Nov 29, 2015
- Fix graph issues · d107727c
  Peter van 't Hof authored 9 years ago
  
  d107727c
- Added index to vt jobs · 6cb4dcbe
  Peter van 't Hof authored 9 years ago
  
  6cb4dcbe
- Style fix · 88d47fcf
  Peter van 't Hof authored 9 years ago
  
  88d47fcf
- Fixed md5sums · 3f7a6044
  Peter van 't Hof authored 9 years ago
  
  3f7a6044
Nov 27, 2015
- Fix dict generate · 32692078
  Peter van 't Hof authored 9 years ago
  
  32692078
- Check for bowtie2-Index files in bowtie2 · 5bc1ea8e
  Wai Yi Leung authored 9 years ago
  
  5bc1ea8e
- Check for bowtie2-Index files in bowtie2 · e945e4db
  Wai Yi Leung authored 9 years ago
  
  e945e4db
- Fix bcftools executeables · 339c0413
  Peter van 't Hof authored 9 years ago
  
  339c0413
Nov 26, 2015
- Fix vcf stats · 7aeda35f
  Peter van 't Hof authored 9 years ago
  
  7aeda35f
- Fix bowtie2 readgroup · ac61c9dd
  Wai Yi Leung authored 9 years ago
  
  ac61c9dd
- changes in tool, since the checking for samples starting with a number went wrong. · 0b6db331
  Sander van der Zeeuw authored 9 years ago
  
  0b6db331
Nov 25, 2015
- Fix default values and conditionals instead of optionals · 92bdf700
  Wai Yi Leung authored 9 years ago
  
  92bdf700
- Fix typo · 8b6724c1
  Peter van 't Hof authored 9 years ago
  
  8b6724c1
- Style fixes · 02639191
  Peter van 't Hof authored 9 years ago
  
  02639191