Commits · f1441306430a3e814cae3db17c954fadfd6c4f76 · Mirrors / biopet.biopet

Mar 09, 2015

Merge branch 'develop' into feature-gentrap · f1441306

bow authored 10 years ago

Conflicts:
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

f1441306

Mar 08, 2015
- Formatting updates · 848279f4
  bow authored 10 years ago
  
  848279f4
- Use correct threads and mem values for Cufflinks and Gsnap wrapper · 08018011
  bow authored 10 years ago
  
  08018011
- Fix bug in JAR run caused by copying entire resource folder · e653337b
  bow authored 10 years ago
  
  e653337b
- Merge branch 'feature-scaladocs' into 'develop' · 5d854a9f
  bow authored 10 years ago
  
  Feature scaladocs Added scala docs to all extensions, utils and pipeline template. See also #37 See merge request !116
  5d854a9f
- Update Cufflinks defaults for cluster run · c0064f43
  bow authored 10 years ago
  
  c0064f43
- Update GSNAP defaults for cluster run · 3ed93bee
  bow authored 10 years ago
  
  3ed93bee
- Update report template · c56d1178
  bow authored 10 years ago
  
  c56d1178
- Add sample-level bam metrics · 8c734d16
  bow authored 10 years ago
  
  8c734d16
- Make sample-level metrics optional, instead of library-level metrics (for RNA) · b2a7573b
  bow authored 10 years ago
  
  b2a7573b
- Add library pair information to sample metrics · 9789e9e6
  bow authored 10 years ago
  
  9789e9e6
- Add library-level and sample-level RNA metrics to report · 1de28c56
  bow authored 10 years ago
  
  1de28c56
- Add per-library RNA metrics job when the sample contains more than 1 library · bbaa6236
  bow authored 10 years ago
  
  bbaa6236
- Use MergeSamFiles for all merges · 77e40ed5
  bow authored 10 years ago
  
  77e40ed5
- Default to not using MarkDuplicates PG tag as it creates conflicts when merging BAM files · 6c7c75a7
  bow authored 10 years ago
  
  6c7c75a7
- Use correct alignment file for per-sample CollectRnaSeqMetrics job · 36568da0
  bow authored 10 years ago
  
  36568da0
- Use correct config name for Md5sum override in SummaryQScript · 12b2af39
  bow authored 10 years ago
  
  12b2af39
- Add CollectRnaSeqMetrics summary to main Gentrap summary · 128aa21f
  bow authored 10 years ago
  
  128aa21f
- Fix incorrectly parsed CollectRnaSeqMetrics metrics output · 29c827c7
  bow authored 10 years ago
  
  29c827c7
- Add chart output of CollectRnaSeqMetrics to summary · 151caa0c
  bow authored 10 years ago
  
  151caa0c
Mar 07, 2015
- Initial mapping subsection in report · 8811baae
  bow authored 10 years ago
  
  8811baae
- Avoid repeatedly defining the same latex command · de316ff7
  bow authored 10 years ago
  
  de316ff7
- Use correct sickle value retrieval · 3e956c9c
  bow authored 10 years ago
  
  3e956c9c
- Add all fastqc plots to report · 41883883
  bow authored 10 years ago
  
  41883883
- Add FastQC parser to PDF report template generator · 3c2f3b45
  bow authored 10 years ago
  
  3c2f3b45
- Update report template to output clipped adapter name correctly · 06e9a56a
  bow authored 10 years ago
  
  06e9a56a
- Update Picard metrics parsing to better handle nonexistent files · 7dabaeca
  bow authored 10 years ago
  
  7dabaeca
- Add fallback job when md5sum job fails · 24d23ba1
  bow authored 10 years ago
  
  24d23ba1
- Adding scala docs · d76b3f66
  Peter van 't Hof authored 10 years ago
  
  d76b3f66
- Update Sickle wrapper to parse sickle single-end output · 24b411f6
  bow authored 10 years ago
  
  24b411f6
- Adding scala docs · 5903aff3
  Peter van 't Hof authored 10 years ago
  
  5903aff3
- Remove old netbeans files · 24749608
  Peter van 't Hof authored 10 years ago
  
  24749608
- Catch possible exceptions when parsing table for heatmap plotting · 075878b1
  bow authored 10 years ago
  
  075878b1
Mar 06, 2015
- Use correct types for JSON output in cutadapt summary · 83e4d44a
  bow authored 10 years ago
  
  83e4d44a
- Initial report · fb8373ab
  bow authored 10 years ago
  
  fb8373ab
- Fix missing adapter name in flexiprep summary · 66bf4e3f
  bow authored 10 years ago
  
  66bf4e3f
- Add version to gentrap summary output · 2fb27c1b
  bow authored 10 years ago
  
  2fb27c1b
- Formatting updates · 86171153
  bow authored 10 years ago
  
  86171153
- Fix sickle wrapper bug causing by incorrect flag output · 6827c6b5
  bow authored 10 years ago
  
  6827c6b5
- Update test for fragments_per_gene mode · 219ead09
  bow authored 10 years ago
  
  219ead09