Commits · 097f37b0b94e5c2d6b47c5705272c3ca40b52b92 · Mirrors / biopet.biopet

Feb 16, 2016
- Added check abort step in pipeline · 097f37b0
  Peter van 't Hof authored 9 years ago
  
  097f37b0
- Adding ValidateFastq to flexiprep · 7c863726
  Peter van 't Hof authored 9 years ago
  
  7c863726
Jan 19, 2016
- Update Cutadapt wrapper and style change (camelCaps instead of _) · 3049d572
  Wai Yi Leung authored 9 years ago
  
  3049d572
Dec 15, 2015
- Refactor match statements · 6c3170cc
  Peter van 't Hof authored 9 years ago
  
  6c3170cc
Dec 11, 2015
- 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
- Style fixes · fe542841
  Peter van 't Hof authored 9 years ago
  
  fe542841
Nov 29, 2015
- Fix graph issues · d107727c
  Peter van 't Hof authored 9 years ago
  
  d107727c
Nov 24, 2015
- Bump version to 0.6.0-SNAPSHOT · ac785920
  Peter van 't Hof authored 9 years ago
  
  ac785920
- Bump version to 0.5.0 · c5303e8c
  Peter van 't Hof authored 9 years ago
  
  c5303e8c
Nov 23, 2015
- Bump to 0.5.0-RC2 · 16d2711f
  Peter van 't Hof authored 9 years ago
  
  16d2711f
Nov 19, 2015
- Bumb version to 0.5.0-RC1 · 19a93bbb
  Peter van 't Hof authored 9 years ago
  
  19a93bbb
- Fixed license headers · fceb39a9
  Peter van 't Hof authored 9 years ago
  
  fceb39a9
- Fixed bug in loading the mainClass for biopet tools · 7f424eb9
  Peter van 't Hof authored 9 years ago
  
  7f424eb9
Oct 20, 2015
- Moved function to utils, this might be usefull in other pipelines · 954e0245
  Peter van 't Hof authored 9 years ago
  
  954e0245
Oct 19, 2015
- Use provided exts Set instead of zipExtensions · 6af00416
  bow authored 9 years ago
  
  6af00416
- Remove R1_ext and R2_ext from Flexiprep · 90eaaf09
  bow authored 9 years ago
  
  90eaaf09
- Add error message when a Flexiprep input file does not have the expected structure · 487324b4
  bow authored 9 years ago
  
  487324b4
- Refactor filename and extension retrieval in Flexiprep · b4b6785a
  bow authored 9 years ago
  
  b4b6785a
Oct 15, 2015
- Added jobs to pipejobs · d6272ab2
  Peter van 't Hof authored 9 years ago
  
  d6272ab2
- Code style · c82dc34f
  Peter van 't Hof authored 9 years ago
  
  c82dc34f
- Fix code warnings · 29923378
  Peter van 't Hof authored 9 years ago
  
  29923378
- Fixed version to single end executables · e2a873b6
  Peter van 't Hof authored 9 years ago
  
  e2a873b6
Oct 09, 2015
- Fix zcat for chunking · ca9c7e5c
  Peter van 't Hof authored 9 years ago
  
  ca9c7e5c
- Fix chunking · f4f1f4cb
  Peter van 't Hof authored 9 years ago
  
  f4f1f4cb
Oct 06, 2015
- Fixed tests in flexiprep · 95ae061e
  Peter van 't Hof authored 9 years ago
  
  95ae061e
- Always execute fastqc_qc · 85f7eb91
  Peter van 't Hof authored 9 years ago
  
  85f7eb91
- Added adapters to summary · 2d241e33
  Peter van 't Hof authored 9 years ago
  
  2d241e33
Oct 05, 2015
- Removed out commented tests · b733ff34
  Peter van 't Hof authored 9 years ago
  
  b733ff34
- Remove useless lines · 31822f0a
  Peter van 't Hof authored 9 years ago
  
  31822f0a
- Fix single end dependency · 936e77a0
  Peter van 't Hof authored 9 years ago
  
  936e77a0
Oct 02, 2015
- Fix code style warnings · 52928227
  Peter van 't Hof authored 9 years ago
  
  52928227
- Move input for gzip to stdin to not remove file · 2156f192
  Peter van 't Hof authored 9 years ago
  
  2156f192
- Fixed summary files of flexiprep · 5d5c30c1
  Peter van 't Hof authored 9 years ago
  
  5d5c30c1
Sep 30, 2015
- Removed test · 310b07ef
  Peter van 't Hof authored 9 years ago
  
  310b07ef
Sep 29, 2015
- Switch to fifo pipes · 8ae539f7
  Peter van 't Hof authored 9 years ago
  
  8ae539f7