General refactor Biopet

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala

@@ -22,22 +22,22 @@ import org.broadinstitute.gatk.utils.commandline.Input
 
 trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   @Input(doc = "Python script", required = false)
-  var python_script: File = _
+  var pythonScript: File = _
 
   executable = config("exe", default = "python", submodule = "python", freeVar = false)
 
-  protected var python_script_name: String = _
+  protected var pythonScriptName: String = _
 
   /**
    * checks if script already exist in jar otherwise try to fetch from the jar
    * @param script name / location of script
    */
   def setPythonScript(script: String) {
-    python_script = new File(script)
-    if (!python_script.exists()) {
+    pythonScript = new File(script)
+    if (!pythonScript.exists()) {
       setPythonScript(script, "")
     } else {
-      python_script_name = script
+      pythonScriptName = script
     }
   }
 
@@ -47,17 +47,17 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
    * @param subpackage location of script in jar
    */
   def setPythonScript(script: String, subpackage: String) {
-    python_script_name = script
-    python_script = new File(".queue/tmp/" + subpackage + python_script_name)
-    if (!python_script.getParentFile.exists) python_script.getParentFile.mkdirs
-    val is = getClass.getResourceAsStream(subpackage + python_script_name)
-    val os = new FileOutputStream(python_script)
+    pythonScriptName = script
+    pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName)
+    if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs
+    val is = getClass.getResourceAsStream(subpackage + pythonScriptName)
+    val os = new FileOutputStream(pythonScript)
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
 
   /** return basic command to prefix the complete command with */
   def getPythonCommand: String = {
-    required(executable) + required(python_script)
+    required(executable) + required(pythonScript)
   }
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala

@@ -44,29 +44,29 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with V
 
   @Output(doc = "Output GTF file")
   lazy val outputGtf: File = {
-    require(input != null && output_dir != null,
+    require(input != null && outputDir != null,
       "Can not set Cufflinks GTF output while input file and/or output directory is not defined")
     // cufflinks always outputs a transcripts.gtf file in the output directory
-    new File(output_dir, "transcripts.gtf")
+    new File(outputDir, "transcripts.gtf")
   }
 
   @Output(doc = "Output isoform FPKM file")
   lazy val outputIsoformsFpkm: File = {
-    require(input != null && output_dir != null,
+    require(input != null && outputDir != null,
       "Can not set Cufflinks isoforms.fpkm_tracking output while input file and/or output directory is not defined")
-    new File(output_dir, "isoforms.fpkm_tracking")
+    new File(outputDir, "isoforms.fpkm_tracking")
   }
 
   @Output(doc = "Output GTF file")
   lazy val outputGenesFpkm: File = {
-    require(input != null && output_dir != null,
+    require(input != null && outputDir != null,
       "Can not set Cufflinks genes.fpkm_tracking output while input file and/or output directory is not defined")
     // cufflinks always outputs a genes.fpkm_tracking file in the output directory
-    new File(output_dir, "genes.fpkm_tracking")
+    new File(outputDir, "genes.fpkm_tracking")
   }
 
   /** write all output files to this directory [./] */
-  var output_dir: File = config("output_dir", default = new File("."))
+  var outputDir: File = config("output_dir", default = new File("."))
 
   /** value of random number generator seed [0] */
   var seed: Option[Int] = config("seed")
@@ -75,106 +75,106 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with V
   var GTF: Option[File] = config("GTF")
 
   /** use reference transcript annotation to guide assembly */
-  var GTF_guide: Option[File] = config("GTF_guide")
+  var gtfGuide: Option[File] = config("GTF_guide")
 
   /** ignore all alignment within transcripts in this file */
-  var mask_file: Option[File] = config("mask_file")
+  var maskFile: Option[File] = config("mask_file")
 
   /** use bias correction - reference fasta required [NULL] */
-  var frag_bias_correct: Option[String] = config("frag_bias_correct")
+  var fragBiasCorrect: Option[String] = config("frag_bias_correct")
 
   /** use 'rescue method' for multi-reads (more accurate) [FALSE] */
-  var multi_read_correct: Boolean = config("multi_read_correct", default = false)
+  var multiReadCorrect: Boolean = config("multi_read_correct", default = false)
 
   /** library prep used for input reads [below] */
-  var library_type: Option[String] = config("library_type")
+  var libraryType: Option[String] = config("library_type")
 
   /** Method used to normalize library sizes [below] */
-  var library_norm_method: Option[String] = config("library_norm_method")
+  var libraryNormMethod: Option[String] = config("library_norm_method")
 
   /** average fragment length (unpaired reads only) [200] */
-  var frag_len_mean: Option[Int] = config("frag_len_mean")
+  var fragLenMean: Option[Int] = config("frag_len_mean")
 
   /** fragment length std deviation (unpaired reads only) [80] */
-  var frag_len_std_dev: Option[Int] = config("frag_len_std_dev")
+  var fragLenStdDev: Option[Int] = config("frag_len_std_dev")
 
   /** maximum iterations allowed for MLE calculation [5000] */
-  var max_mle_iterations: Option[Int] = config("max_mle_iterations")
+  var maxMleIterations: Option[Int] = config("max_mle_iterations")
 
   /** count hits compatible with reference RNAs only [FALSE] */
-  var compatible_hits_norm: Boolean = config("compatible_hits_norm", default = false)
+  var compatibleHitsNorm: Boolean = config("compatible_hits_norm", default = false)
 
   /** count all hits for normalization [TRUE] */
-  var total_hits_norm: Boolean = config("total_hits_norm", default = true)
+  var totalHitsNorm: Boolean = config("total_hits_norm", default = true)
 
   /** Number of fragment generation samples [100] */
-  var num_frag_count_draws: Option[Int] = config("num_frag_count_draws")
+  var numFragCountDraws: Option[Int] = config("num_frag_count_draws")
 
   /** Number of fragment assignment samples per generation [50] */
-  var num_frag_assign_draws: Option[Int] = config("num_frag_assign_draws")
+  var numFragAssignDraws: Option[Int] = config("num_frag_assign_draws")
 
   /** Maximum number of alignments allowed per fragment [unlim] */
-  var max_frag_multihits: Option[Int] = config("max_frag_multihits")
+  var maxFragMultihits: Option[Int] = config("max_frag_multihits")
 
   /** No effective length correction [FALSE] */
-  var no_effective_length_correction: Boolean = config("no_effective_length_correction", default = false)
+  var noEffectiveLengthCorrection: Boolean = config("no_effective_length_correction", default = false)
 
   /** No length correction [FALSE] */
-  var no_length_correction: Boolean = config("no_length_correction", default = false)
+  var noLengthCorrection: Boolean = config("no_length_correction", default = false)
 
   /** assembled transcripts have this ID prefix [CUFF] */
   var label: Option[String] = config("label")
 
   /** suppress transcripts below this abundance level [0.10] */
-  var min_isoform_fraction: Option[Float] = config("min_isoform_fraction")
+  var minIsoformFraction: Option[Float] = config("min_isoform_fraction")
 
   /** suppress intra-intronic transcripts below this level [0.15] */
-  var pre_mrna_fraction: Option[Float] = config("pre_mrna_fraction")
+  var preMrnaFraction: Option[Float] = config("pre_mrna_fraction")
 
   /** ignore alignments with gaps longer than this [300000] */
-  var max_intron_length: Option[Int] = config("max_intron_length")
+  var maxIntronLength: Option[Int] = config("max_intron_length")
 
   /** alpha for junction binomial test filter [0.001] */
-  var junc_alpha: Option[Float] = config("junc_alpha")
+  var juncAlpha: Option[Float] = config("junc_alpha")
 
   /** percent read overhang taken as 'suspiciously small' [0.09] */
-  var small_anchor_fraction: Option[Float] = config("small_anchor_fraction")
+  var smallAnchorFraction: Option[Float] = config("small_anchor_fraction")
 
   /** minimum number of fragments needed for new transfrags [10] */
-  var min_frags_per_transfrag: Option[Int] = config("min_frags_per_transfrag")
+  var minFragsPerTransfrag: Option[Int] = config("min_frags_per_transfrag")
 
   /** number of terminal exon bp to tolerate in introns [8] */
-  var overhang_tolerance: Option[Int] = config("overhang_tolerance")
+  var overhangTolerance: Option[Int] = config("overhang_tolerance")
 
   /** maximum genomic length allowed for a given bundle [3500000] */
-  var max_bundle_length: Option[Int] = config("max_bundle_length")
+  var maxBundleLength: Option[Int] = config("max_bundle_length")
 
   /** maximum fragments allowed in a bundle before skipping [500000] */
-  var max_bundle_frags: Option[Int] = config("max_bundle_frags")
+  var maxBundleFrags: Option[Int] = config("max_bundle_frags")
 
   /** minimum intron size allowed in genome [50] */
-  var min_intron_length: Option[Int] = config("min_intron_length")
+  var minIntronLength: Option[Int] = config("min_intron_length")
 
   /** minimum avg coverage required to attempt 3' trimming [10] */
-  var trim_3_avgcov_thresh: Option[Int] = config("trim_3_avgcov_thresh")
+  var trim3AvgCovThresh: Option[Int] = config("trim_3_avgcov_thresh")
 
   /** fraction of avg coverage below which to trim 3' end [0.1] */
-  var trim_3_dropoff_frac: Option[Float] = config("trim_3_dropoff_frac")
+  var trim3DropOffFrac: Option[Float] = config("trim_3_dropoff_frac")
 
   /** maximum fraction of allowed multireads per transcript [0.75] */
-  var max_multiread_fraction: Option[Float] = config("max_multiread_fraction")
+  var maxMultireadFraction: Option[Float] = config("max_multiread_fraction")
 
   /** maximum gap size to fill between transfrags (in bp) [50] */
-  var overlap_radius: Option[Int] = config("overlap_radius")
+  var overlapRadius: Option[Int] = config("overlap_radius")
 
   /** disable tiling by faux reads [FALSE] */
-  var no_faux_reads: Boolean = config("no_faux_reads", default = false)
+  var noFauxReads: Boolean = config("no_faux_reads", default = false)
 
   /** overhang allowed on 3' end when merging with reference [600] */
-  var flag_3_overhang_tolerance: Option[Int] = config("flag_3_overhang_tolerance")
+  var flag3OverhangTolerance: Option[Int] = config("flag_3_overhang_tolerance")
 
   /** overhang allowed inside reference intron when merging [30] */
-  var intron_overhang_tolerance: Option[Int] = config("intron_overhang_tolerance")
+  var intronOverhangTolerance: Option[Int] = config("intron_overhang_tolerance")
 
   /** log-friendly verbose processing (no progress bar) [FALSE] */
   var verbose: Boolean = config("verbose", default = false)
@@ -183,7 +183,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with V
   var quiet: Boolean = config("quiet", default = false)
 
   /** do not contact server to check for update availability [FALSE] */
-  var no_update_check: Boolean = config("no_update_check", default = false)
+  var noUpdateCheck: Boolean = config("no_update_check", default = false)
 
   def versionRegex = """cufflinks v(.*)""".r
   def versionCommand = executable
@@ -191,46 +191,46 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with V
 
   def cmdLine =
     required(executable) +
-      required("--output-dir", output_dir) +
+      required("--output-dir", outputDir) +
       optional("--num-threads", threads) +
       optional("--seed", seed) +
       optional("--GTF", GTF) +
-      optional("--GTF-guide", GTF_guide) +
-      optional("--mask-file", mask_file) +
-      optional("--frag-bias-correct", frag_bias_correct) +
-      conditional(multi_read_correct, "--multi-read-correct") +
-      optional("--library-type", library_type) +
-      optional("--library-norm-method", library_norm_method) +
-      optional("--frag-len-mean", frag_len_mean) +
-      optional("--frag-len-std-dev", frag_len_std_dev) +
-      optional("--max-mle-iterations", max_mle_iterations) +
-      conditional(compatible_hits_norm, "--compatible-hits-norm") +
-      conditional(total_hits_norm, "--total-hits-norm") +
-      optional("--num-frag-count-draws", num_frag_count_draws) +
-      optional("--num-frag-assign-draws", num_frag_assign_draws) +
-      optional("--max-frag-multihits", max_frag_multihits) +
-      conditional(no_effective_length_correction, "--no-effective-length-correction") +
-      conditional(no_length_correction, "--no-length-correction") +
+      optional("--GTF-guide", gtfGuide) +
+      optional("--mask-file", maskFile) +
+      optional("--frag-bias-correct", fragBiasCorrect) +
+      conditional(multiReadCorrect, "--multi-read-correct") +
+      optional("--library-type", libraryType) +
+      optional("--library-norm-method", libraryNormMethod) +
+      optional("--frag-len-mean", fragLenMean) +
+      optional("--frag-len-std-dev", fragLenStdDev) +
+      optional("--max-mle-iterations", maxMleIterations) +
+      conditional(compatibleHitsNorm, "--compatible-hits-norm") +
+      conditional(totalHitsNorm, "--total-hits-norm") +
+      optional("--num-frag-count-draws", numFragCountDraws) +
+      optional("--num-frag-assign-draws", numFragAssignDraws) +
+      optional("--max-frag-multihits", maxFragMultihits) +
+      conditional(noEffectiveLengthCorrection, "--no-effective-length-correction") +
+      conditional(noLengthCorrection, "--no-length-correction") +
       optional("--label", label) +
-      optional("--min-isoform-fraction", min_isoform_fraction) +
-      optional("--pre-mrna-fraction", pre_mrna_fraction) +
-      optional("--max-intron-length", max_intron_length) +
-      optional("--junc-alpha", junc_alpha) +
-      optional("--small-anchor-fraction", small_anchor_fraction) +
-      optional("--min-frags-per-transfrag", min_frags_per_transfrag) +
-      optional("--overhang-tolerance", overhang_tolerance) +
-      optional("--max-bundle-length", max_bundle_length) +
-      optional("--max-bundle-frags", max_bundle_frags) +
-      optional("--min-intron-length", min_intron_length) +
-      optional("--trim-3-avgcov-thresh", trim_3_avgcov_thresh) +
-      optional("--trim-3-dropoff-frac", trim_3_dropoff_frac) +
-      optional("--max-multiread-fraction", max_multiread_fraction) +
-      optional("--overlap-radius", overlap_radius) +
-      conditional(no_faux_reads, "--no-faux-reads") +
-      optional("--flag-3-overhang-tolerance", flag_3_overhang_tolerance) +
-      optional("--intron-overhang-tolerance", intron_overhang_tolerance) +
+      optional("--min-isoform-fraction", minIsoformFraction) +
+      optional("--pre-mrna-fraction", preMrnaFraction) +
+      optional("--max-intron-length", maxIntronLength) +
+      optional("--junc-alpha", juncAlpha) +
+      optional("--small-anchor-fraction", smallAnchorFraction) +
+      optional("--min-frags-per-transfrag", minFragsPerTransfrag) +
+      optional("--overhang-tolerance", overhangTolerance) +
+      optional("--max-bundle-length", maxBundleLength) +
+      optional("--max-bundle-frags", maxBundleFrags) +
+      optional("--min-intron-length", minIntronLength) +
+      optional("--trim-3-avgcov-thresh", trim3AvgCovThresh) +
+      optional("--trim-3-dropoff-frac", trim3DropOffFrac) +
+      optional("--max-multiread-fraction", maxMultireadFraction) +
+      optional("--overlap-radius", overlapRadius) +
+      conditional(noFauxReads, "--no-faux-reads") +
+      optional("--flag-3-overhang-tolerance", flag3OverhangTolerance) +
+      optional("--intron-overhang-tolerance", intronOverhangTolerance) +
       conditional(verbose, "--verbose") +
       conditional(quiet, "--quiet") +
-      conditional(no_update_check, "--no-update-check") +
+      conditional(noUpdateCheck, "--no-update-check") +
       required(input)
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala

@@ -40,46 +40,46 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
 
   /** input GTF file */
   @Input(doc = "Input GTF file", required = true)
-  var transcripts_gtf: File = null
+  var transcriptsGtf: File = null
 
   /** output file, computed automatically from output directory */
   @Output(doc = "Output CXB file")
   lazy val outputCxb: File = {
-    require(output_dir != null,
+    require(outputDir != null,
       "Can not set Cuffquant CXB output while input file and/or output directory is not defined")
     // cufflinks always outputs a transcripts.gtf file in the output directory
-    new File(output_dir, "abundances.cxb")
+    new File(outputDir, "abundances.cxb")
   }
 
   /** write all output files to this directory [./] */
-  var output_dir: File = config("output_dir", default = new File("."))
+  var outputDir: File = config("output_dir", default = new File("."))
 
   /** ignore all alignment within transcripts in this file */
-  var mask_file: Option[File] = config("mask_file")
+  var maskFile: Option[File] = config("mask_file")
 
   /** use bias correction - reference fasta required [NULL] */
-  var frag_bias_correct: Option[String] = config("frag_bias_correct")
+  var fragBiasCorrect: Option[String] = config("frag_bias_correct")
 
   /** use 'rescue method' for multi-reads (more accurate) [FALSE] */
-  var multi_read_correct: Boolean = config("multi_read_correct", default = false)
+  var multiReadCorrect: Boolean = config("multi_read_correct", default = false)
 
   /** number of threads used during analysis [1] */
-  var num_threads: Option[Int] = config("num_threads")
+  var numThreads: Option[Int] = config("num_threads")
 
   /** library prep used for input reads [below] */
-  var library_type: Option[String] = config("library_type")
+  var libraryType: Option[String] = config("library_type")
 
   /** average fragment length (unpaired reads only) [200] */
-  var frag_len_mean: Option[Int] = config("frag_len_mean")
+  var fragLenMean: Option[Int] = config("frag_len_mean")
 
   /** fragment length std deviation (unpaired reads only) [80] */
-  var frag_len_std_dev: Option[Int] = config("frag_len_std_dev")
+  var fragLenStdDev: Option[Int] = config("frag_len_std_dev")
 
   /** minimum number of alignments in a locus for testing [10] */
-  var min_alignment_count: Option[Int] = config("min_alignment_count")
+  var minAlignmentCount: Option[Int] = config("min_alignment_count")
 
   /** maximum iterations allowed for MLE calculation [5000] */
-  var max_mle_iterations: Option[Int] = config("max_mle_iterations")
+  var maxMleIterations: Option[Int] = config("max_mle_iterations")
 
   /** log-friendly verbose processing (no progress bar) [FALSE] */
   var verbose: Boolean = config("verbose", default = false)
@@ -91,31 +91,31 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
   var seed: Option[Int] = config("seed")
 
   /** do not contact server to check for update availability [FALSE] */
-  var no_update_check: Boolean = config("no_update_check", default = false)
+  var noUpdateCheck: Boolean = config("no_update_check", default = false)
 
   /** maximum fragments allowed in a bundle before skipping [500000] */
-  var max_bundle_frags: Option[Int] = config("max_bundle_frags")
+  var maxBundleFrags: Option[Int] = config("max_bundle_frags")
 
   /** Maximum number of alignments allowed per fragment [unlim] */
-  var max_frag_multihits: Option[Int] = config("max_frag_multihits")
+  var maxFragMultihits: Option[Int] = config("max_frag_multihits")
 
   /** No effective length correction [FALSE] */
-  var no_effective_length_correction: Boolean = config("no_effective_length_correction", default = false)
+  var noEffectiveLengthCorrection: Boolean = config("no_effective_length_correction", default = false)
 
   /** No length correction [FALSE] */
-  var no_length_correction: Boolean = config("no_length_correction", default = false)
+  var noLengthCorrection: Boolean = config("no_length_correction", default = false)
 
   /** Skip a random subset of reads this size [0.0] */
-  var read_skip_fraction: Option[Double] = config("read_skip_fraction")
+  var readSkipFraction: Option[Double] = config("read_skip_fraction")
 
   /** Break all read pairs [FALSE] */
-  var no_read_pairs: Boolean = config("no_read_pairs", default = false)
+  var noReadPairs: Boolean = config("no_read_pairs", default = false)
 
   /** Trim reads to be this long (keep 5' end) [none] */
-  var trim_read_length: Option[Int] = config("trim_read_length")
+  var trimReadLength: Option[Int] = config("trim_read_length")
 
   /** Disable SCV correction */
-  var no_scv_correction: Boolean = config("no_scv_correction", default = false)
+  var noScvCorrection: Boolean = config("no_scv_correction", default = false)
 
   def versionRegex = """cuffquant v(.*)""".r
   def versionCommand = executable
@@ -123,28 +123,28 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
 
   def cmdLine =
     required(executable) +
-      required("--output-dir", output_dir) +
-      optional("--mask-file", mask_file) +
-      optional("--frag-bias-correct", frag_bias_correct) +
-      conditional(multi_read_correct, "--multi-read-correct") +
-      optional("--num-threads", num_threads) +
-      optional("--library-type", library_type) +
-      optional("--frag-len-mean", frag_len_mean) +
-      optional("--frag-len-std-dev", frag_len_std_dev) +
-      optional("--min-alignment-count", min_alignment_count) +
-      optional("--max-mle-iterations", max_mle_iterations) +
+      required("--output-dir", outputDir) +
+      optional("--mask-file", maskFile) +
+      optional("--frag-bias-correct", fragBiasCorrect) +
+      conditional(multiReadCorrect, "--multi-read-correct") +
+      optional("--num-threads", numThreads) +
+      optional("--library-type", libraryType) +
+      optional("--frag-len-mean", fragLenMean) +
+      optional("--frag-len-std-dev", fragLenStdDev) +
+      optional("--min-alignment-count", minAlignmentCount) +
+      optional("--max-mle-iterations", maxMleIterations) +
       conditional(verbose, "--verbose") +
       conditional(quiet, "--quiet") +
       optional("--seed", seed) +
-      conditional(no_update_check, "--no-update-check") +
-      optional("--max-bundle-frags", max_bundle_frags) +
-      optional("--max-frag-multihits", max_frag_multihits) +
-      conditional(no_effective_length_correction, "--no-effective-length-correction") +
-      conditional(no_length_correction, "--no-length-correction") +
-      optional("--read-skip-fraction", read_skip_fraction) +
-      conditional(no_read_pairs, "--no-read-pairs") +
-      optional("--trim-read-length", trim_read_length) +
-      conditional(no_scv_correction, "--no-scv-correction") +
-      required(transcripts_gtf) +
+      conditional(noUpdateCheck, "--no-update-check") +
+      optional("--max-bundle-frags", maxBundleFrags) +
+      optional("--max-frag-multihits", maxFragMultihits) +
+      conditional(noEffectiveLengthCorrection, "--no-effective-length-correction") +
+      conditional(noLengthCorrection, "--no-length-correction") +
+      optional("--read-skip-fraction", readSkipFraction) +
+      conditional(noReadPairs, "--no-read-pairs") +
+      optional("--trim-read-length", trimReadLength) +
+      conditional(noScvCorrection, "--no-scv-correction") +
+      required(transcriptsGtf) +
       required(input.map(_.mkString(";").mkString(" ")))
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -192,7 +192,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
       "bpoutput" -> 0,
       "toomanyn" -> 0
     )
-    val adapter_stats: mutable.Map[String, Long] = mutable.Map()
+    val adapterStats: mutable.Map[String, Long] = mutable.Map()
 
     if (statsOutput.exists) {
       val statsFile = Source.fromFile(statsOutput)
@@ -206,7 +206,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
           case tooManyN(m)              => stats("toomanyn") = m.replaceAll(",", "").toLong
           case basePairsProcessed(m)    => stats("bpinput") = m.replaceAll(",", "").toLong
           case basePairsWritten(m)      => stats("bpoutput") = m.replaceAll(",", "").toLong
-          case adapterR(adapter, count) => adapter_stats += (adapter -> count.toLong)
+          case adapterR(adapter, count) => adapterStats += (adapter -> count.toLong)
           case _                        =>
         }
       }
@@ -224,7 +224,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
       "num_reads_discarded_many_n" -> stats("toomanyn"),
       "num_bases_input" -> stats("bpinput"),
       "num_based_output" -> stats("bpoutput"),
-      adaptersStatsName -> adapter_stats.toMap
+      adaptersStatsName -> adapterStats.toMap
     )
   }
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -40,7 +40,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
   var output: File = null
 
   executable = config("exe", default = "fastqc")
-  var java_exe: String = config("exe", default = "java", submodule = "java", freeVar = false)
+  var javaExe: String = config("exe", default = "java", submodule = "java", freeVar = false)
   var kmers: Option[Int] = config("kmers")
   var quiet: Boolean = config("quiet", default = false)
   var noextract: Boolean = config("noextract", default = false)
@@ -85,7 +85,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
 
   /** return commandline to execute */
   def cmdLine = required(executable) +
-    optional("--java", java_exe) +
+    optional("--java", javaExe) +
     optional("--threads", threads) +
     optional("--contaminants", contaminants) +
     optional("--adapters", adapters) +

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -31,22 +31,22 @@ import scala.io.Source
  */
 class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
   @Input(doc = "R1 input")
-  var input_R1: File = _
+  var inputR1: File = _
 
   @Input(doc = "R2 input", required = false)
-  var input_R2: File = _
+  var inputR2: File = _
 
   @Output(doc = "R1 output", required = false)
-  var output_R1: File = _
+  var outputR1: File = _
 
   @Output(doc = "R2 output", required = false)
-  var output_R2: File = _
+  var outputR2: File = _
 
   @Output(doc = "singles output", required = false)
-  var output_singles: File = _
+  var outputSingles: File = _
 
   @Output(doc = "stats output")
-  var output_stats: File = _
+  var outputStats: File = _
 
   executable = config("exe", default = "sickle", freeVar = false)
   var qualityType: Option[String] = config("qualitytype")
@@ -67,22 +67,22 @