Commit 16f002bc authored 8 years ago by bow

Merge branch 'feature-downloadsample_gears' into 'develop'

Feature downloadsample gears

This is a change on request for project 122

See merge request !415

parents bb8b4550 daeedb39

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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 11 additions, 4 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala 4 additions, 3 deletions

...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala 88 additions, 0 deletions

.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala 47 additions, 0 deletions

...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala 6 additions, 1 deletion

...a/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala 14 additions, 8 deletions

...c/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala 1 addition, 0 deletions

...ls/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
docs/pipelines/gears.md 3 additions, 0 deletions

docs/pipelines/gears.md
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala 10 additions, 2 deletions

...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala 4 additions, 6 deletions

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala 76 additions, 21 deletions

...ain/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala 21 additions, 6 deletions

...l/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala 90 additions, 0 deletions

.../nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala 15 additions, 0 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala 12 additions, 4 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKrakenTest.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/pipelines/gears/GearsKrakenTest.scala
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosedTest.scala 1 addition, 1 deletion

...mc/sasc/biopet/pipelines/gears/GearsQiimeClosedTest.scala
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala 132 additions, 66 deletions

...nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala 40 additions, 14 deletions

...scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
pom.xml 1 addition, 0 deletions

pom.xml

with 577 additions and 137 deletions

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