Merge remote-tracking branch 'remotes/origin/fix-generate_indexes' into feature_annotation_versions
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- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala 28 additions, 0 deletions...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala 36 additions, 0 deletions...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala 1 addition, 2 deletions...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala 46 additions, 0 deletions...l/lumc/sasc/biopet/extensions/picard/NormalizeFasta.scala
- biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala 2 additions, 2 deletions...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala 51 additions, 0 deletions...c/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
- biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala 2 additions, 1 deletion...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala 97 additions, 0 deletions...cala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
- biopet-tools/src/test/resources/GCF_000844745.1.report 23 additions, 0 deletionsbiopet-tools/src/test/resources/GCF_000844745.1.report
- biopet-tools/src/test/resources/NC_003403.1.fasta 22 additions, 0 deletionsbiopet-tools/src/test/resources/NC_003403.1.fasta
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala 33 additions, 0 deletions.../nl/lumc/sasc/biopet/tools/DownloadNcbiAssemblyTest.scala
- generate-indexes/pom.xml 1 addition, 1 deletiongenerate-indexes/pom.xml
- generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala 265 additions, 0 deletions...sc/biopet/pipelines/generateindexes/DownloadGenomes.scala
- generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala 114 additions, 269 deletions...sc/biopet/pipelines/generateindexes/GenerateIndexes.scala
- generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala 69 additions, 24 deletions...iopet/pipelines/generateindexes/DownloadGenomesTest.scala
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