Commits · 1de28c56ba4f2a61a20c5d2f986fb49b1b47eeda · Mirrors / biopet.biopet · GitLab

08 Mar, 2015 9 commits
- Add library-level and sample-level RNA metrics to report · 1de28c56
  bow authored Mar 08, 2015
  
  1de28c56
- Add per-library RNA metrics job when the sample contains more than 1 library · bbaa6236
  bow authored Mar 08, 2015
  
  bbaa6236
- Use MergeSamFiles for all merges · 77e40ed5
  bow authored Mar 08, 2015
  
  77e40ed5
- Default to not using MarkDuplicates PG tag as it creates conflicts when merging BAM files · 6c7c75a7
  bow authored Mar 08, 2015
  
  6c7c75a7
- Use correct alignment file for per-sample CollectRnaSeqMetrics job · 36568da0
  bow authored Mar 08, 2015
  
  36568da0
- Use correct config name for Md5sum override in SummaryQScript · 12b2af39
  bow authored Mar 08, 2015
  
  12b2af39
- Add CollectRnaSeqMetrics summary to main Gentrap summary · 128aa21f
  bow authored Mar 08, 2015
  
  128aa21f
- Fix incorrectly parsed CollectRnaSeqMetrics metrics output · 29c827c7
  bow authored Mar 08, 2015
  
  29c827c7
- Add chart output of CollectRnaSeqMetrics to summary · 151caa0c
  bow authored Mar 08, 2015
  
  151caa0c
07 Mar, 2015 10 commits
- Initial mapping subsection in report · 8811baae
  bow authored Mar 07, 2015
  
  8811baae
- Avoid repeatedly defining the same latex command · de316ff7
  bow authored Mar 07, 2015
  
  de316ff7
- Use correct sickle value retrieval · 3e956c9c
  bow authored Mar 07, 2015
  
  3e956c9c
- Add all fastqc plots to report · 41883883
  bow authored Mar 07, 2015
  
  41883883
- Add FastQC parser to PDF report template generator · 3c2f3b45
  bow authored Mar 07, 2015
  
  3c2f3b45
- Update report template to output clipped adapter name correctly · 06e9a56a
  bow authored Mar 07, 2015
  
  06e9a56a
- Update Picard metrics parsing to better handle nonexistent files · 7dabaeca
  bow authored Mar 07, 2015
  
  7dabaeca
- Add fallback job when md5sum job fails · 24d23ba1
  bow authored Mar 07, 2015
  
  24d23ba1
- Update Sickle wrapper to parse sickle single-end output · 24b411f6
  bow authored Mar 07, 2015
  
  24b411f6
- Catch possible exceptions when parsing table for heatmap plotting · 075878b1
  bow authored Mar 07, 2015
  
  075878b1
06 Mar, 2015 16 commits
- Use correct types for JSON output in cutadapt summary · 83e4d44a
  bow authored Mar 06, 2015
  
  83e4d44a
- Initial report · fb8373ab
  bow authored Mar 06, 2015
  
  fb8373ab
- Fix missing adapter name in flexiprep summary · 66bf4e3f
  bow authored Mar 06, 2015
  
  66bf4e3f
- Add version to gentrap summary output · 2fb27c1b
  bow authored Mar 06, 2015
  
  2fb27c1b
- Formatting updates · 86171153
  bow authored Mar 06, 2015
  
  86171153
- Fix sickle wrapper bug causing by incorrect flag output · 6827c6b5
  bow authored Mar 06, 2015
  
  6827c6b5
- Update test for fragments_per_gene mode · 219ead09
  bow authored Mar 06, 2015
  
  219ead09
- Further trim down tests · 1c953ac1
  bow authored Mar 06, 2015
  
  1c953ac1
- Add convenience methods for creating sample configs · 2d0050ea
  bow authored Mar 06, 2015
  
  2d0050ea
- Trim down general test to test for expMeasure and strandProtocol combinations · c7cd5499
  bow authored Mar 06, 2015
  
  c7cd5499
- Add more config options to test in GentrapTest · 76ef30d0
  bow authored Mar 06, 2015
  
  76ef30d0
- Fix duplicate value on valid cufflinks measures · a207d0b6
  bow authored Mar 06, 2015
  
  a207d0b6
- Remove addAllJobs from CufflinksProducer · 10873179
  bow authored Mar 06, 2015
  
  10873179
- Refactor Cufflinks jobs into its own trait · acdacee9
  bow authored Mar 06, 2015
  
  acdacee9
- Add general heatmap plotting fallback when error is encountered · dbc78f53
  bow authored Mar 06, 2015
  
  dbc78f53
- Rename for consistency · e5dd66c8
  bow authored Mar 06, 2015
  
  e5dd66c8
05 Mar, 2015 5 commits
- Update formatting · 51031007
  bow authored Mar 05, 2015
  
  51031007
- Initial update for GentrapTest · 497eef6f
  bow authored Mar 05, 2015
  
  497eef6f
- Avoid NullPointerException when checking for R2 in Gentrap · e714e45d
  bow authored Mar 05, 2015
  
  e714e45d
- Put all expression table outputs into a single directory · 40eeaa44
  bow authored Mar 05, 2015
  
  40eeaa44
- Add heatmap plot jobs for all output · 393af584
  bow authored Mar 05, 2015
  
  393af584