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biopet.biopet
Commits
biopet-biopet
public
gentrap
src
main
scala
nl
lumc
sasc
biopet
pipelines
gentrap
Gentrap.scala
04 Apr, 2015
2 commits
Add reference files to Gentrap summary
· 2a338501
bow
authored
Apr 04, 2015
2a338501
Refactor Gentrap reference checking
· e9393c0d
bow
authored
Apr 04, 2015
e9393c0d
23 Mar, 2015
2 commits
Update docs in main Gentrap pipeline
· 172b0345
bow
authored
Mar 23, 2015
172b0345
Use package version in Gentrap
· c30670ae
bow
authored
Mar 23, 2015
c30670ae
20 Mar, 2015
1 commit
Set idsorting job as intermediate
· 68eefc48
bow
authored
Mar 20, 2015
68eefc48
13 Mar, 2015
4 commits
Use correct directory for checking dict file in Gentrap
· 1fb00ca7
bow
authored
Mar 13, 2015
1fb00ca7
Update Gentrap dict test to be more test-friendly
· bbbaecd3
bow
authored
Mar 13, 2015
bbbaecd3
Add check to ensure dict file is present in Gentrap
· 0453d301
bow
authored
Mar 13, 2015
0453d301
Set default cutadapt minimum_length to 20 in Gentrap
· 6ffdacf9
bow
authored
Mar 13, 2015
6ffdacf9
12 Mar, 2015
1 commit
Default to disabling MarkDuplicates in Gentrap
· 0267b656
bow
authored
Mar 12, 2015
0267b656
10 Mar, 2015
1 commit
Fix missing wiggle jobs
· 8bed40ff
bow
authored
Mar 10, 2015
8bed40ff
09 Mar, 2015
2 commits
Formatting updates
· 1c9c025e
bow
authored
Mar 09, 2015
1c9c025e
Update gentrap summary and stats
· 4b348b21
bow
authored
Mar 09, 2015
4b348b21
08 Mar, 2015
9 commits
Formatting updates
· 848279f4
bow
authored
Mar 08, 2015
848279f4
Add sample-level bam metrics
· 8c734d16
bow
authored
Mar 08, 2015
8c734d16
Make sample-level metrics optional, instead of library-level metrics (for RNA)
· b2a7573b
bow
authored
Mar 08, 2015
b2a7573b
Add library pair information to sample metrics
· 9789e9e6
bow
authored
Mar 08, 2015
9789e9e6
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
Add CollectRnaSeqMetrics summary to main Gentrap summary
· 128aa21f
bow
authored
Mar 08, 2015
128aa21f
06 Mar, 2015
4 commits
Add version to gentrap summary output
· 2fb27c1b
bow
authored
Mar 06, 2015
2fb27c1b
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
Rename for consistency
· e5dd66c8
bow
authored
Mar 06, 2015
e5dd66c8
05 Mar, 2015
9 commits
Update formatting
· 51031007
bow
authored
Mar 05, 2015
51031007
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
Use scalaz's implicit option for boolean
· 67ae06c1
bow
authored
Mar 05, 2015
67ae06c1
Initial heat map plotting
· e7764348
bow
authored
Mar 05, 2015
e7764348
Add job for writing PDF report
· 6d78e827
bow
authored
Mar 05, 2015
6d78e827
Formatting updates
· cf117dac
bow
authored
Mar 05, 2015
cf117dac
Add PDF template writing job to main Gentrap
· 6f33fef8
bow
authored
Mar 05, 2015
6f33fef8
04 Mar, 2015
5 commits
Disable untested expMeasure modes
· b660ab1c
bow
authored
Mar 04, 2015
b660ab1c
Expose enum-based config values as public attributes
· 6b22cc16
bow
authored
Mar 04, 2015
6b22cc16
Formatting updates
· 32816835
bow
authored
Mar 04, 2015
32816835
Add variant calling jobs and expose its output as attribute and in summary
· 062f17b7
bow
authored
Mar 04, 2015
062f17b7
Fix bug that omits md5sum calculation of Flexiprep files
· f6cb0ae0
bow
authored
Mar 04, 2015
f6cb0ae0