diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala similarity index 99% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala index 00362623a7e780439539e30798ec288d56751f3b..6f77445113df364f2a7f2ffb06bbeca60702a505 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala @@ -1,5 +1,6 @@ - /* +/* * Copyright (c) 2012 The Broad Institute +* Modifications (c) 2014 Leiden University Medical Center * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala similarity index 100% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/BiopetQScript.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Config.scala similarity index 100% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Config.scala diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala similarity index 100% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/PipelineCommand.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala similarity index 94% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala index a9371cb61defc460cb642da9058038be3b2530b4..b6d6cbc002f1507f005f28cbcc17efe31056f55d 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Ln.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers +package nl.lumc.sasc.biopet.function import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.InProcessFunction diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala similarity index 97% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala index 5bda85e172ee2e46cdb7ed4b296f430de8b63aec..90eaca4fb8af4a023c8f402dc03e2696ef97d880 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Python.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers +package nl.lumc.sasc.biopet.function import java.io.FileOutputStream import nl.lumc.sasc.biopet.core._ diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala similarity index 94% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala index 2dded92c27894439efcd51b61da07ec1c5fa7db0..a3b546a5e616cc83d75d0be43d8d240dab65570a 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Sha1sum.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers +package nl.lumc.sasc.biopet.function import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala similarity index 94% rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala index 206d4bd0dfa639a297af03d798af7fa6dbd75c9e..33b407671a121e9fa7af0f721784a3b4f4ded780 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers +package nl.lumc.sasc.biopet.function import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala similarity index 98% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala index c4c407ec342116958e962f4128bc07ab125ba7b7..ca436d089e839698a6d02e0a96c31539c19ad0a8 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Cutadapt.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers.fastq +package nl.lumc.sasc.biopet.function.fastq import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala similarity index 98% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala index 36e2e16d7947168a481a2ae1c80e61d91d1f04d0..16c4b9d9e21575e0f492d0141cadbb5b5911e7d6 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Fastqc.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers.fastq +package nl.lumc.sasc.biopet.function.fastq import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala similarity index 98% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala index b8a9d5335a3d9de571faee6c970d2dc783cd44b1..92a098a508c89fceb0349a0abc26fbcd520da45e 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/wrappers/fastq/Sickle.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers.fastq +package nl.lumc.sasc.biopet.function.fastq import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala similarity index 99% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala index c46e4f14b2d44a1309aea99ed53c7650ab20104d..876fa8cacb6c4b29e4547e0f72cac27ff1f551e8 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala @@ -1,8 +1,8 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep import nl.lumc.sasc.biopet.core._ -import nl.lumc.sasc.biopet.wrappers._ -import nl.lumc.sasc.biopet.wrappers.fastq._ +import nl.lumc.sasc.biopet.function._ +import nl.lumc.sasc.biopet.function.fastq._ import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.picard._ diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala similarity index 96% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala index 3defa15fcfed88c4f89e03b62cf6e7a293683770..3180785a393e73683471c076f73b033bb036298a 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala @@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts //import java.io.FileOutputStream import nl.lumc.sasc.biopet.core._ -import nl.lumc.sasc.biopet.wrappers._ +import nl.lumc.sasc.biopet.function._ import org.broadinstitute.sting.queue.function.CommandLineFunction import org.broadinstitute.sting.commandline._ import java.io.File diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala similarity index 96% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala index a0c4e9ff273918894d72f72ae824d700453f59e5..1ab9b00b5ff425b59adc693221543f1e9b7a8992 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala @@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction -import nl.lumc.sasc.biopet.wrappers.Python +import nl.lumc.sasc.biopet.function.Python import org.broadinstitute.sting.commandline._ import java.io.File diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala similarity index 95% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala index 346d88d90d1e011b400d564cd9a101e525e00d2c..da7594b5c9f783818a0104d50466ad0582082678 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala @@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction -import nl.lumc.sasc.biopet.wrappers.Python +import nl.lumc.sasc.biopet.function.Python import org.broadinstitute.sting.commandline._ import java.io.File diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala similarity index 96% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala index b046872d29f81b1d70c4625dae82fcc66f8f3cd1..7e6a4c094c6535194d575b1a4bde6b8036abfdd2 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala @@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction -import nl.lumc.sasc.biopet.wrappers.Python +import nl.lumc.sasc.biopet.function.Python import org.broadinstitute.sting.commandline._ import java.io.File diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala similarity index 96% rename from flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala rename to flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala index 2375ffaff99180a7f6d7140e5989b6276d418dc9..a25832abe14ac921a9ee1f57aa047e2b20080339 100644 --- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala @@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction -import nl.lumc.sasc.biopet.wrappers.Python +import nl.lumc.sasc.biopet.function.Python import org.broadinstitute.sting.commandline._ import java.io.File diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala similarity index 99% rename from gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala rename to gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala index a0402a2b21f4ee332b4d5597c80799e3cbf0e38a..8b4c32e5a6acc08caf2dd5a98a0ccbcef59cd913 100644 --- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala +++ b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala @@ -1,7 +1,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk -import nl.lumc.sasc.biopet.wrappers._ -import nl.lumc.sasc.biopet.wrappers.aligners._ +import nl.lumc.sasc.biopet.function._ +import nl.lumc.sasc.biopet.function.aligners._ import nl.lumc.sasc.biopet.core._ import nl.lumc.sasc.biopet.pipelines.mapping._ import nl.lumc.sasc.biopet.pipelines.flexiprep._ diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala b/gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala similarity index 100% rename from gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala rename to gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala similarity index 97% rename from mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala rename to mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala index f6a5e70f147b057dfe96c9de6ccfa7d3eb3d9c8f..d1dae66e33af50e5d3be1da8d2586ebc96ff957a 100644 --- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala +++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers.aligners +package nl.lumc.sasc.biopet.function.aligners import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala similarity index 98% rename from mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala rename to mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala index 54e2928fca81e767ffc85baedde2ad83ec2209ba..492c0413bf6ff29593a5c9829eb64325d0a1feca 100644 --- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala +++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala @@ -1,4 +1,4 @@ -package nl.lumc.sasc.biopet.wrappers.aligners +package nl.lumc.sasc.biopet.function.aligners import nl.lumc.sasc.biopet.core._ import org.broadinstitute.sting.queue.function.CommandLineFunction diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala similarity index 99% rename from mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala rename to mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala index bd774d4311d15aae4731c0b3a02c3e2ad374ff32..d8174acac9a0fb925a85ce9543022d373d37b409 100644 --- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala +++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala @@ -1,7 +1,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping -import nl.lumc.sasc.biopet.wrappers._ -import nl.lumc.sasc.biopet.wrappers.aligners._ +import nl.lumc.sasc.biopet.function._ +import nl.lumc.sasc.biopet.function.aligners._ import java.util.Date import nl.lumc.sasc.biopet.core._ import nl.lumc.sasc.biopet.pipelines.flexiprep._