Commits · 8a2421602432b2780e883165639c7be595638e4c · Mirrors / biopet.biopet

Aug 04, 2014
- fix on test file · 8a242160
  Peter van 't Hof authored 10 years ago
  
  8a242160
- Fix on outputdir for flexiprep · a0e16b2f
  Peter van 't Hof authored 10 years ago
  
  a0e16b2f
- Use of new constructors · 7c1fa255
  Peter van 't Hof authored 10 years ago
  
  7c1fa255
- Added constructor and moved Lazy variables in 1 function · 123e830e
  Peter van 't Hof authored 10 years ago
  
  123e830e
- Added mkdir on outputDir · b975df6e
  Peter van 't Hof authored 10 years ago
  
  b975df6e
- Added contructor · e5d44e32
  Peter van 't Hof authored 10 years ago
  
  e5d44e32
- Added SeqtkSeq function to Flexiprep · 43c985ef
  Peter van 't Hof authored 10 years ago
  
  43c985ef
Jul 30, 2014
- Wrappers are now split in general and specific flexiprep extensions · 6b5c4320
  Peter van 't Hof authored 10 years ago
  
  6b5c4320
- Changed config back because of compatibility issues · a2275bd4
  Peter van 't Hof authored 10 years ago
  
  a2275bd4
- Remove unused imports · 3748001f
  Peter van 't Hof authored 10 years ago
  
  3748001f
- Update style and exclude JSON defs from style reformatting · 19b4d9eb
  bow authored 10 years ago
  
  19b4d9eb
- Style reformatting · 19f47e48
  bow authored 10 years ago
  
  19f47e48
- Fix bug in Flexiprep python summary script · df98d70a
  bow authored 10 years ago
  
  df98d70a
Jul 29, 2014
- Fix flexiprep summary json parsing · 2b595c2c
  bow authored 10 years ago
  
  2b595c2c
- Fix on output directories of sha1sum and seqstat · 0aabeb73
  bow authored 10 years ago
  
  0aabeb73
- Fix Ln import with new namespace · b121e619
  bow authored 10 years ago
  
  b121e619
- Merge remote-tracking branch 'upstream/peter' · 526c6d93
  bow authored 10 years ago
  
  Conflicts: biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqtk.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/SeqtkSeq.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
  526c6d93
- Flexiprep passes jobs to new summary · 397a0a5d
  Peter van 't Hof authored 10 years ago
  
  397a0a5d
- Add gentrap scripts · 85e3f91d
  bow authored 10 years ago
  
  85e3f91d
- Add initial gentrap main interface · b840a916
  bow authored 10 years ago
  
  b840a916
- Update base BiopetQScript command line argument names · a90b06da
  bow authored 10 years ago
  
  a90b06da
- Fix Gentrap pom.xml · c0598153
  bow authored 10 years ago
  
  c0598153
- Use relative paths in empty cutadapt commands · 7731bd62
  bow authored 10 years ago
  
  7731bd62
- Use relative symlinks by default in Flexiprep final files · deac9640
  bow authored 10 years ago
  
  deac9640
- Add relative symlink option to Ln wrapper · 7b260498
  bow authored 10 years ago
  
  7b260498
- changed function to extensions · dd4f0175
  Peter van 't Hof authored 10 years ago
  
  dd4f0175
- Initial checkin for Gentrap · 1a6df3ca
  bow authored 10 years ago
  
  1a6df3ca
- Seqstat now uses quality type data · 3501d2eb
  Peter van 't Hof authored 10 years ago
  
  3501d2eb
- Function to get encoding of the fastq file, replaces python script · f0f070f7
  Peter van 't Hof authored 10 years ago
  
  f0f070f7
Jul 28, 2014
- Seqstat now uses quality type data · 8e67bf4f
  Peter van 't Hof authored 10 years ago
  
  8e67bf4f
- Update Seqtk wrapper namespace · 1cc49dfc
  bow authored 10 years ago
  
  1cc49dfc
- Update scripts default location to follow Maven convention · 210c6b69
  bow authored 10 years ago
  
  210c6b69
- Update flexiprep summary file name · c6b4115d
  bow authored 10 years ago
  
  c6b4115d
- Output cutadapt statistics correctly in summary files · 556fc8c1
  bow authored 10 years ago
  
  556fc8c1
- Merge commit 'cde8f1a6 ' into peter · 7a45bbcd
  Peter van 't Hof authored 10 years ago
  
  7a45bbcd
- Fix on fastqc jobs · cde8f1a6
  Peter van 't Hof authored 10 years ago
  
  cde8f1a6
- Revert "Fix on fastqc jobs" · 373dbb5c
  Peter van 't Hof authored 10 years ago
  
  This reverts commit 5945ab1746a433f4c9c2100176934d7ee86c38a2.
  373dbb5c
- Fix on fastqc jobs · 613343f7
  Peter van 't Hof authored 10 years ago
  
  613343f7
- Switch to functions · e7f818e2
  Peter van 't Hof authored 10 years ago
  
  e7f818e2
- Fix on output variable · 1395457c
  Peter van 't Hof authored 10 years ago
  
  1395457c