From c8f56975ada77e4e0348ada253d1d502d4d9d4ae Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 14 Mar 2016 16:19:57 +0100
Subject: [PATCH] General refactor Biopet
---
.../PythonCommandLineFunction.scala | 22 +-
.../sasc/biopet/extensions/Cufflinks.scala | 152 ++++----
.../sasc/biopet/extensions/Cuffquant.scala | 84 ++---
.../sasc/biopet/extensions/Cutadapt.scala | 6 +-
.../lumc/sasc/biopet/extensions/Fastqc.scala | 4 +-
.../lumc/sasc/biopet/extensions/Sickle.scala | 28 +-
.../nl/lumc/sasc/biopet/extensions/Star.scala | 38 +-
.../lumc/sasc/biopet/extensions/Tophat.scala | 350 +++++++++---------
.../extensions/VariantEffectPredictor.scala | 160 ++++----
.../biopet/extensions/bowtie/Bowtie.scala | 4 +-
.../biopet/extensions/bowtie/Bowtie2.scala | 120 +++---
.../breakdancer/BreakdancerConfig.scala | 32 +-
.../biopet/extensions/conifer/Conifer.scala | 2 +-
.../extensions/conifer/ConiferAnalyze.scala | 4 +-
.../sasc/biopet/extensions/gmap/Gsnap.scala | 304 +++++++--------
.../biopet/extensions/kraken/Kraken.scala | 8 +-
.../extensions/kraken/KrakenReport.scala | 4 +-
.../extensions/macs2/Macs2CallPeak.scala | 24 +-
.../extensions/pindel/PindelCaller.scala | 24 +-
.../extensions/qiime/AssignTaxonomy.scala | 80 ++--
.../extensions/qiime/MergeOtuMaps.scala | 4 +-
.../qiime/PickClosedReferenceOtus.scala | 24 +-
.../biopet/extensions/qiime/PickOtus.scala | 200 +++++-----
.../biopet/extensions/qiime/PickRepSet.scala | 8 +-
.../qiime/SplitLibrariesFastq.scala | 44 +--
.../extensions/sambamba/SambambaMarkdup.scala | 20 +-
.../extensions/sambamba/SambambaMerge.scala | 4 +-
.../extensions/sambamba/SambambaView.scala | 4 +-
.../nl/lumc/sasc/biopet/tools/SeqStat.scala | 6 +-
.../sasc/biopet/tools/VepNormalizer.scala | 6 +-
.../biopet/tools/AnnotateVcfWithBedTest.scala | 12 +-
.../biopet/tools/BastyGenerateFastaTest.scala | 16 +-
.../tools/CheckAllelesVcfInBamTest.scala | 12 +-
.../sasc/biopet/tools/GvcfToBedTest.scala | 18 +-
.../sasc/biopet/tools/MergeAllelesTest.scala | 12 +-
.../sasc/biopet/tools/MpileupToVcfTest.scala | 6 +-
.../sasc/biopet/tools/SummaryToTsvTest.scala | 12 +-
.../lumc/sasc/biopet/tools/VcfToTsvTest.scala | 16 +-
.../sasc/biopet/tools/VcfWithVcfTest.scala | 28 +-
.../sasc/biopet/tools/VepNormalizerTest.scala | 26 +-
.../pipelines/flexiprep/Flexiprep.scala | 104 +++---
.../pipelines/flexiprep/QcCommand.scala | 8 +-
.../pipelines/flexiprep/FlexiprepTest.scala | 2 +-
.../sasc/biopet/pipelines/gears/Gears.scala | 4 +-
.../biopet/pipelines/gears/GearsKraken.scala | 10 +-
.../pipelines/gears/GearsQiimeClosed.scala | 2 +-
.../pipelines/gears/GearsQiimeRtax.scala | 8 +-
.../biopet/pipelines/gears/GearsSingle.scala | 2 +-
.../biopet/pipelines/gentrap/Gentrap.scala | 4 +-
.../gentrap/measures/CufflinksGuided.scala | 2 +-
.../measures/CufflinksMeasurement.scala | 6 +-
.../biopet/pipelines/mapping/Mapping.scala | 76 ++--
.../mapping/MultisampleMappingTrait.scala | 8 +-
.../pipelines/mapping/MappingTest.scala | 8 +-
.../sasc/biopet/pipelines/sage/Sage.scala | 4 +-
.../pipelines/shiva/svcallers/Pindel.scala | 4 +-
56 files changed, 1090 insertions(+), 1090 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 69131561e..e4c0b2695 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
+++ b/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)
}
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
index 9177b7a6b..4eb907f3c 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/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)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
index d7ead689a..6ac11bc43 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+++ b/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(" ")))
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index 777cfb53f..60c25a5a6 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/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
)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 8906bf134..ee3751631 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/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) +
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index f6571f220..9ed1b0538 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/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 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
/** Return command to execute */
def cmdLine = {
var cmd: String = required(executable)
- if (input_R2 != null) {
+ if (inputR2 != null) {
cmd += required("pe") +
- required("-r", input_R2) +
- required("-p", output_R2) +
- required("-s", output_singles)
+ required("-r", inputR2) +
+ required("-p", outputR2) +
+ required("-s", outputSingles)
} else cmd += required("se")
cmd +
- (if (inputAsStdin) required("-f", new File("/dev/stdin")) else required("-f", input_R1)) +
+ (if (inputAsStdin) required("-f", new File("/dev/stdin")) else required("-f", inputR1)) +
required("-t", qualityType) +
- (if (outputAsStsout) required("-o", new File("/dev/stdout")) else required("-o", output_R1)) +
+ (if (outputAsStsout) required("-o", new File("/dev/stdout")) else required("-o", outputR1)) +
optional("-q", qualityThreshold) +
optional("-l", lengthThreshold) +
conditional(noFiveprime, "-x") +
conditional(discardN, "-n") +
conditional(quiet || outputAsStsout, "--quiet") +
- (if (outputAsStsout) "" else " > " + required(output_stats))
+ (if (outputAsStsout) "" else " > " + required(outputStats))
}
/** returns stats map for summary */
@@ -98,7 +98,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
var stats: mutable.Map[String, Int] = mutable.Map()
- if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines()) {
+ if (outputStats.exists) for (line <- Source.fromFile(outputStats).getLines()) {
line match {
// single run
case sKept(num) => stats += ("num_reads_kept" -> num.toInt)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 916e2b4c9..913c95b7b 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -146,24 +146,24 @@ object Star {
outputDir: File,
isIntermediate: Boolean = false,
deps: List[File] = Nil): (File, List[Star]) = {
- val starCommand_pass1 = Star(configurable, R1, R2, new File(outputDir, "aln-pass1"))
- starCommand_pass1.isIntermediate = isIntermediate
- starCommand_pass1.deps = deps
- starCommand_pass1.beforeGraph()
-
- val starCommand_reindex = new Star(configurable)
- starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
- starCommand_reindex.outputDir = new File(outputDir, "re-index")
- starCommand_reindex.runmode = "genomeGenerate"
- starCommand_reindex.isIntermediate = isIntermediate
- starCommand_reindex.beforeGraph()
-
- val starCommand_pass2 = Star(configurable, R1, R2, new File(outputDir, "aln-pass2"))
- starCommand_pass2.genomeDir = starCommand_reindex.outputDir
- starCommand_pass2.isIntermediate = isIntermediate
- starCommand_pass2.deps = deps
- starCommand_pass2.beforeGraph()
-
- (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
+ val starCommandPass1 = Star(configurable, R1, R2, new File(outputDir, "aln-pass1"))
+ starCommandPass1.isIntermediate = isIntermediate
+ starCommandPass1.deps = deps
+ starCommandPass1.beforeGraph()
+
+ val starCommandReindex = new Star(configurable)
+ starCommandReindex.sjdbFileChrStartEnd = starCommandPass1.outputTab
+ starCommandReindex.outputDir = new File(outputDir, "re-index")
+ starCommandReindex.runmode = "genomeGenerate"
+ starCommandReindex.isIntermediate = isIntermediate
+ starCommandReindex.beforeGraph()
+
+ val starCommandPass2 = Star(configurable, R1, R2, new File(outputDir, "aln-pass2"))
+ starCommandPass2.genomeDir = starCommandReindex.outputDir
+ starCommandPass2.isIntermediate = isIntermediate
+ starCommandPass2.deps = deps
+ starCommandPass2.beforeGraph()
+
+ (starCommandPass2.outputSam, List(starCommandPass1, starCommandReindex, starCommandPass2))
}
}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index 495049da7..83a2b386f 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -42,330 +42,330 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Refe
var R2: List[File] = List.empty[File]
private def checkInputsOk(): Unit =
- require(R1.nonEmpty && output_dir != null, "Read 1 input(s) are defined and output directory is defined")
+ require(R1.nonEmpty && outputDir != null, "Read 1 input(s) are defined and output directory is defined")
/** output files, computed automatically from output directory */
@Output(doc = "Output SAM/BAM file")
lazy val outputAcceptedHits: File = {
checkInputsOk()
- new File(output_dir, if (no_convert_bam) "accepted_hits.sam" else "accepted_hits.bam")
+ new File(outputDir, if (noConvertBam) "accepted_hits.sam" else "accepted_hits.bam")
}
@Output(doc = "Unmapped SAM/BAM file")
lazy val outputUnmapped: File = {
checkInputsOk()
- new File(output_dir, if (no_convert_bam) "unmapped.sam" else "unmapped.bam")
+ new File(outputDir, if (noConvertBam) "unmapped.sam" else "unmapped.bam")
}
@Output(doc = "Deletions BED file")
lazy val outputDeletions: File = {
checkInputsOk()
- new File(output_dir, "deletions.bed")
+ new File(outputDir, "deletions.bed")
}
@Output(doc = "Insertions BED file")
lazy val outputInsertions: File = {
checkInputsOk()
- new File(output_dir, "insertions.bed")
+ new File(outputDir, "insertions.bed")
}
@Output(doc = "Junctions BED file")
lazy val outputJunctions: File = {
checkInputsOk()
- new File(output_dir, "junctions.bed")
+ new File(outputDir, "junctions.bed")
}
@Output(doc = "Alignment summary file")
lazy val outputAlignSummary: File = {
checkInputsOk()
- new File(output_dir, "align_summary.txt")
+ new File(outputDir, "align_summary.txt")
}
@Argument(doc = "Bowtie index", shortName = "bti", required = true)
- var bowtie_index: String = config("bowtie_index")
+ var bowtieIndex: String = config("bowtie_index")
/** write all output files to this directory [./] */
- var output_dir: File = config("output_dir", default = new File("tophat_out"))
+ var outputDir: File = config("output_dir", default = new File("tophat_out"))
var bowtie1: Boolean = config("bowtie1", default = false)
- var read_mismatches: Option[Int] = config("read_mismatches")
+ var readMismatches: Option[Int] = config("read_mismatches")
- var read_gap_length: Option[Int] = config("read_gap_length")
+ var readGapLength: Option[Int] = config("read_gap_length")
- var read_edit_dist: Option[Int] = config("read_edit_dist")
+ var readEditDist: Option[Int] = config("read_edit_dist")
- var read_realign_edit_dist: Option[Int] = config("read_realign_edit_dist")
+ var readRealignEditDist: Option[Int] = config("read_realign_edit_dist")
- var min_anchor: Option[Int] = config("min_anchor")
+ var minAnchor: Option[Int] = config("min_anchor")
- var splice_mismatches: Option[String] = config("splice_mismatches")
+ var spliceMismatches: Option[String] = config("splice_mismatches")
- var min_intron_length: Option[Int] = config("min_intron_length")
+ var minIntronLength: Option[Int] = config("min_intron_length")
- var max_intron_length: Option[Int] = config("max_intron_length")
+ var maxIntronLength: Option[Int] = config("max_intron_length")
- var max_multihits: Option[Int] = config("max_multihits")
+ var maxMultihits: Option[Int] = config("max_multihits")
- var suppress_hits: Boolean = config("suppress_hits", default = false)
+ var suppressHits: Boolean = config("suppress_hits", default = false)
- var transcriptome_max_hits: Option[Int] = config("transcriptome_max_hits")
+ var transcriptomeMaxHits: Option[Int] = config("transcriptome_max_hits")
- var prefilter_multihits: Boolean = config("prefilter_multihits", default = false)
+ var preFilterMultihits: Boolean = config("prefilter_multihits", default = false)
- var max_insertion_length: Option[Int] = config("max_insertion_length")
+ var maxInsertionLength: Option[Int] = config("max_insertion_length")
- var max_deletion_length: Option[Int] = config("max_deletion_length")
+ var maxDeletionLength: Option[Int] = config("max_deletion_length")
- var solexa_quals: Boolean = config("solexa_quals", default = false)
+ var solexaQuals: Boolean = config("solexa_quals", default = false)
- var solexa1_3_quals: Boolean = config("solexa1.3_quals", default = false)
+ var solexa13Quals: Boolean = config("solexa1.3_quals", default = false)
- var phred64_quals: Boolean = config("phred64_quals", default = false)
+ var phred64Quals: Boolean = config("phred64_quals", default = false)
var quals: Boolean = config("quals", default = false)
- var integer_quals: Boolean = config("integer_quals", default = false)
+ var integerQuals: Boolean = config("integer_quals", default = false)
var color: Boolean = config("color", default = false)
- var color_out: Boolean = config("color_out", default = false)
+ var colorOut: Boolean = config("color_out", default = false)
- var library_type: Option[String] = config("library_type")
+ var libraryType: Option[String] = config("library_type")
var resume: Option[String] = config("resume")
var GTF: Option[String] = config("GTF")
- var transcriptome_index: Option[String] = config("transcriptome_index")
+ var transcriptomeIndex: Option[String] = config("transcriptome_index")
- var transcriptome_only: Boolean = config("transcriptome_only", default = false)
+ var transcriptomeOnly: Boolean = config("transcriptome_only", default = false)
- var raw_juncs: Option[String] = config("raw_juncs")
+ var rawJuncs: Option[String] = config("raw_juncs")
var insertions: Option[String] = config("insertions")
var deletions: Option[String] = config("deletions")
- var mate_inner_dist: Option[Int] = config("mate_inner_dist")
+ var mateInnerDist: Option[Int] = config("mate_inner_dist")
- var mate_std_dev: Option[Int] = config("mate_std_dev")
+ var mateStdDev: Option[Int] = config("mate_std_dev")
- var no_novel_juncs: Boolean = config("no_novel_juncs", default = false)
+ var noNovelJuncs: Boolean = config("no_novel_juncs", default = false)
- var no_novel_indels: Boolean = config("no_novel_indels", default = false)
+ var noNovelIndels: Boolean = config("no_novel_indels", default = false)
- var no_gtf_juncs: Boolean = config("no_gtf_juncs", default = false)
+ var noGtfJuncs: Boolean = config("no_gtf_juncs", default = false)
- var no_coverage_search: Boolean = config("no_coverage_search", default = false)
+ var noCoverageSearch: Boolean = config("no_coverage_search", default = false)
- var coverage_search: Boolean = config("coverage_search", default = false)
+ var coverageSearch: Boolean = config("coverage_search", default = false)
- var microexon_search: Boolean = config("microexon_search", default = false)
+ var microexonSearch: Boolean = config("microexon_search", default = false)
- var keep_tmp: Boolean = config("keep_tmp", default = false)
+ var keepTmp: Boolean = config("keep_tmp", default = false)
- var tmp_dir: Option[String] = config("tmp_dir")
+ var tmpDir: Option[String] = config("tmp_dir")
var zpacker: Option[String] = config("zpacker")
- var unmapped_fifo: Boolean = config("unmapped_fifo", default = false)
+ var unmappedFifo: Boolean = config("unmapped_fifo", default = false)
- var report_secondary_alignments: Boolean = config("report_secondary_alignments", default = false)
+ var reportSecondaryAlignments: Boolean = config("report_secondary_alignments", default = false)
- var no_discordant: Boolean = config("no_discordant", default = false)
+ var noDiscordant: Boolean = config("no_discordant", default = false)
- var no_mixed: Boolean = config("no_mixed", default = false)
+ var noMixed: Boolean = config("no_mixed", default = false)
- var segment_mismatches: Option[Int] = config("segment_mismatches")
+ var segmentMismatches: Option[Int] = config("segment_mismatches")
- var segment_length: Option[Int] = config("segment_length")
+ var segmentLength: Option[Int] = config("segment_length")
- var bowtie_n: Boolean = config("bowtie_n", default = false)
+ var bowtieN: Boolean = config("bowtie_n", default = false)
- var min_coverage_intron: Option[Int] = config("min_coverage_intron")
+ var minCoverageIntron: Option[Int] = config("min_coverage_intron")
- var max_coverage_intron: Option[Int] = config("max_coverage_intron")
+ var maxCoverageIntron: Option[Int] = config("max_coverage_intron")
- var min_segment_intron: Option[Int] = config("min_segment_intron")
+ var minSegmentIntron: Option[Int] = config("min_segment_intron")
- var max_segment_intron: Option[Int] = config("max_segment_intron")
+ var maxSegmentIntron: Option[Int] = config("max_segment_intron")
- var no_sort_bam: Boolean = config("no_sort_bam", default = false)
+ var noSortBam: Boolean = config("no_sort_bam", default = false)
- var no_convert_bam: Boolean = config("no_convert_bam", default = false)
+ var noConvertBam: Boolean = config("no_convert_bam", default = false)
- var keep_fasta_order: Boolean = config("keep_fasta_order", default = false)
+ var keepFastaOrder: Boolean = config("keep_fasta_order", default = false)
- var allow_partial_mapping: Boolean = config("allow_partial_mapping", default = false)
+ var allowPartialMapping: Boolean = config("allow_partial_mapping", default = false)
- var b2_very_fast: Boolean = config("b2_very_fast", default = false)
+ var b2VeryFast: Boolean = config("b2_very_fast", default = false)
- var b2_fast: Boolean = config("b2_fast", default = false)
+ var b2Fast: Boolean = config("b2_fast", default = false)
- var b2_sensitive: Boolean = config("b2_sensitive", default = false)
+ var b2Sensitive: Boolean = config("b2_sensitive", default = false)
- var b2_very_sensitive: Boolean = config("b2_very_sensitive", default = false)
+ var b2VerySensitive: Boolean = config("b2_very_sensitive", default = false)
- var b2_N: Option[Int] = config("b2_N")
+ var b2N: Option[Int] = config("b2_N")
- var b2_L: Option[Int] = config("b2_L")
+ var b2L: Option[Int] = config("b2_L")
- var b2_i: Option[String] = config("b2_i")
+ var b2I: Option[String] = config("b2_i")
- var b2_n_ceil: Option[String] = config("b2_n_ceil")
+ var b2NCeil: Option[String] = config("b2_n_ceil")
- var b2_gbar: Option[Int] = config("b2_gbar")
+ var b2Gbar: Option[Int] = config("b2_gbar")
- var b2_mp: Option[String] = config("b2_mp")
+ var b2Mp: Option[String] = config("b2_mp")
- var b2_np: Option[Int] = config("b2_np")
+ var b2Np: Option[Int] = config("b2_np")
- var b2_rdg: Option[String] = config("b2_rdg")
+ var b2Rdg: Option[String] = config("b2_rdg")
- var b2_rfg: Option[String] = config("b2_rfg")
+ var b2Rfg: Option[String] = config("b2_rfg")
- var b2_score_min: Option[String] = config("b2_score_min")
+ var b2ScoreMin: Option[String] = config("b2_score_min")
- var b2_D: Option[Int] = config("b2_D")
+ var b2D: Option[Int] = config("b2_D")
- var b2_R: Option[Int] = config("b2_R")
+ var b2R: Option[Int] = config("b2_R")
- var fusion_search: Boolean = config("fusion_search", default = false)
+ var fusionSearch: Boolean = config("fusion_search", default = false)
- var fusion_anchor_length: Option[Int] = config("fusion_anchor_length")
+ var fusionAnchorLength: Option[Int] = config("fusion_anchor_length")
- var fusion_min_dist: Option[Int] = config("fusion_min_dist")
+ var fusionMinDist: Option[Int] = config("fusion_min_dist")
- var fusion_read_mismatches: Option[Int] = config("fusion_read_mismatches")
+ var fusionReadMismatches: Option[Int] = config("fusion_read_mismatches")
- var fusion_multireads: Option[Int] = config("fusion_multireads")
+ var fusionMultireads: Option[Int] = config("fusion_multireads")
- var fusion_multipairs: Option[Int] = config("fusion_multipairs")
+ var fusionMultipairs: Option[Int] = config("fusion_multipairs")
- var fusion_ignore_chromosomes: Option[String] = config("fusion_ignore_chromosomes")
+ var fusionIgnoreChromosomes: Option[String] = config("fusion_ignore_chromosomes")
- var fusion_do_not_resolve_conflicts: Boolean = config("fusion_do_not_resolve_conflicts", default = false)
+ var fusionDoNotResolveConflicts: Boolean = config("fusion_do_not_resolve_conflicts", default = false)
- var rg_id: Option[String] = config("rg_id")
+ var rgId: Option[String] = config("rg_id")
- var rg_sample: Option[String] = config("rg_sample")
+ var rgSample: Option[String] = config("rg_sample")
- var rg_library: Option[String] = config("rg_library")
+ var rgLibrary: Option[String] = config("rg_library")
- var rg_description: Option[String] = config("rg_description")
+ var rgDescription: Option[String] = config("rg_description")
- var rg_platform_unit: Option[String] = config("rg_platform_unit")
+ var rgPlatformUnit: Option[String] = config("rg_platform_unit")
- var rg_center: Option[String] = config("rg_center")
+ var rgCenter: Option[String] = config("rg_center")
- var rg_date: Option[String] = config("rg_date")
+ var rgDate: Option[String] = config("rg_date")
- var rg_platform: Option[String] = config("rg_platform")
+ var rgPlatform: Option[String] = config("rg_platform")
override def beforeGraph: Unit = {
super.beforeGraph
- if (bowtie1 && !new File(bowtie_index).getParentFile.list().toList
- .filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".ebwt")))
+ if (bowtie1 && !new File(bowtieIndex).getParentFile.list().toList
+ .filter(_.startsWith(new File(bowtieIndex).getName)).exists(_.endsWith(".ebwt")))
throw new IllegalArgumentException("No bowtie1 index found for tophat")
- else if (!new File(bowtie_index).getParentFile.list().toList
- .filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".bt2")))
+ else if (!new File(bowtieIndex).getParentFile.list().toList
+ .filter(_.startsWith(new File(bowtieIndex).getName)).exists(_.endsWith(".bt2")))
throw new IllegalArgumentException("No bowtie2 index found for tophat")
}
def cmdLine: String = required(executable) +
- optional("-o", output_dir) +
+ optional("-o", outputDir) +
conditional(bowtie1, "--bowtie1") +
- optional("--read-mismatches", read_mismatches) +
- optional("--read-gap-length", read_gap_length) +
- optional("--read-edit-dist", read_edit_dist) +
- optional("--read-realign-edit-dist", read_realign_edit_dist) +
- optional("--min-anchor", min_anchor) +
- optional("--splice-mismatches", splice_mismatches) +
- optional("--min-intron-length", min_intron_length) +
- optional("--max-intron-length", max_intron_length) +
- optional("--max-multihits", max_multihits) +
- conditional(suppress_hits, "--suppress-hits") +
- optional("--transcriptome-max-hits", transcriptome_max_hits) +
- conditional(prefilter_multihits, "--prefilter-multihits") +
- optional("--max-insertion-length", max_insertion_length) +
- optional("--max-deletion-length", max_deletion_length) +
- conditional(solexa_quals, "--solexa-quals") +
- conditional(solexa1_3_quals, "--solexa1.3-quals") +
- conditional(phred64_quals, "--phred64-quals") +
+ optional("--read-mismatches", readMismatches) +
+ optional("--read-gap-length", readGapLength) +
+ optional("--read-edit-dist", readEditDist) +
+ optional("--read-realign-edit-dist", readRealignEditDist) +
+ optional("--min-anchor", minAnchor) +
+ optional("--splice-mismatches", spliceMismatches) +
+ optional("--min-intron-length", minIntronLength) +
+ optional("--max-intron-length", maxIntronLength) +
+ optional("--max-multihits", maxMultihits) +
+ conditional(suppressHits, "--suppress-hits") +
+ optional("--transcriptome-max-hits", transcriptomeMaxHits) +
+ conditional(preFilterMultihits, "--prefilter-multihits") +
+ optional("--max-insertion-length", maxInsertionLength) +
+ optional("--max-deletion-length", maxDeletionLength) +
+ conditional(solexaQuals, "--solexa-quals") +
+ conditional(solexa13Quals, "--solexa1.3-quals") +
+ conditional(phred64Quals, "--phred64-quals") +
conditional(quals, "--quals") +
- conditional(integer_quals, "--integer-quals") +
+ conditional(integerQuals, "--integer-quals") +
conditional(color, "--color") +
- conditional(color_out, "--color-out") +
- optional("--library-type", library_type) +
+ conditional(colorOut, "--color-out") +
+ optional("--library-type", libraryType) +
optional("--num-threads", threads) +
optional("--resume", resume) +
optional("--GTF", GTF) +
- optional("--transcriptome-index", transcriptome_index) +
- conditional(transcriptome_only, "--transcriptome-only") +
- optional("--raw-juncs", raw_juncs) +
+ optional("--transcriptome-index", transcriptomeIndex) +
+ conditional(transcriptomeOnly, "--transcriptome-only") +
+ optional("--raw-juncs", rawJuncs) +
optional("--insertions", insertions) +
optional("--deletions", deletions) +
- optional("--mate-inner-dist", mate_inner_dist) +
- optional("--mate-std-dev", mate_std_dev) +
- conditional(no_novel_juncs, "--no-novel-juncs") +
- conditional(no_novel_indels, "--no-novel-indels") +
- conditional(no_gtf_juncs, "--no-gtf-juncs") +
- conditional(no_coverage_search, "--no-coverage-search") +
- conditional(coverage_search, "--coverage-search") +
- conditional(microexon_search, "--microexon-search") +
- conditional(keep_tmp, "--keep-tmp") +
- optional("--tmp-dir", tmp_dir) +
+ optional("--mate-inner-dist", mateInnerDist) +
+ optional("--mate-std-dev", mateStdDev) +
+ conditional(noNovelJuncs, "--no-novel-juncs") +
+ conditional(noNovelIndels, "--no-novel-indels") +
+ conditional(noGtfJuncs, "--no-gtf-juncs") +
+ conditional(noCoverageSearch, "--no-coverage-search") +
+ conditional(coverageSearch, "--coverage-search") +
+ conditional(microexonSearch, "--microexon-search") +
+ conditional(keepTmp, "--keep-tmp") +
+ optional("--tmp-dir", tmpDir) +
optional("--zpacker", zpacker) +
- conditional(unmapped_fifo, "--unmapped-fifo") +
- conditional(report_secondary_alignments, "--report-secondary-alignments") +
- conditional(no_discordant, "--no-discordant") +
- conditional(no_mixed, "--no-mixed") +
- optional("--segment-mismatches", segment_mismatches) +
- optional("--segment-length", segment_length) +
- conditional(bowtie_n, "--bowtie-n") +
- optional("--min-coverage-intron", min_coverage_intron) +
- optional("--max-coverage-intron", max_coverage_intron) +
- optional("--min-segment-intron", min_segment_intron) +
- optional("--max-segment-intron", max_segment_intron) +
- conditional(no_sort_bam, "--no-sort-bam") +
- conditional(no_convert_bam, "--no-convert-bam") +
- conditional(keep_fasta_order, "--keep-fasta-order") +
- conditional(allow_partial_mapping, "--allow-partial-mapping") +
- conditional(b2_very_fast, "--b2-very-fast") +
- conditional(b2_fast, "--b2-fast") +
- conditional(b2_sensitive, "--b2-sensitive") +
- conditional(b2_very_sensitive, "--b2-very-sensitive") +
- optional("--b2-N", b2_N) +
- optional("--b2-L", b2_L) +
- optional("--b2-i", b2_i) +
- optional("--b2-n-ceil", b2_n_ceil) +
- optional("--b2-gbar", b2_gbar) +
- optional("--b2-mp", b2_mp) +
- optional("--b2-np", b2_np) +
- optional("--b2-rdg", b2_rdg) +
- optional("--b2-rfg", b2_rfg) +
- optional("--b2-score-min", b2_score_min) +
- optional("--b2-D", b2_D) +
- optional("--b2-R", b2_R) +
- conditional(fusion_search, "--fusion-search") +
- optional("--fusion-anchor-length", fusion_anchor_length) +
- optional("--fusion-min-dist", fusion_min_dist) +
- optional("--fusion-read-mismatches", fusion_read_mismatches) +
- optional("--fusion-multireads", fusion_multireads) +
- optional("--fusion-multipairs", fusion_multipairs) +
- optional("--fusion-ignore-chromosomes", fusion_ignore_chromosomes) +
- conditional(fusion_do_not_resolve_conflicts, "--fusion-do-not-resolve-conflicts") +
- optional("--rg-id", rg_id) +
- optional("--rg-sample", rg_sample) +
- optional("--rg-library", rg_library) +
- optional("--rg-description", rg_description) +
- optional("--rg-platform-unit", rg_platform_unit) +
- optional("--rg-center", rg_center) +
- optional("--rg-date", rg_date) +
- optional("--rg-platform", rg_platform) +
- required(bowtie_index) +
+ conditional(unmappedFifo, "--unmapped-fifo") +
+ conditional(reportSecondaryAlignments, "--report-secondary-alignments") +
+ conditional(noDiscordant, "--no-discordant") +
+ conditional(noMixed, "--no-mixed") +
+ optional("--segment-mismatches", segmentMismatches) +
+ optional("--segment-length", segmentLength) +
+ conditional(bowtieN, "--bowtie-n") +
+ optional("--min-coverage-intron", minCoverageIntron) +
+ optional("--max-coverage-intron", maxCoverageIntron) +
+ optional("--min-segment-intron", minSegmentIntron) +
+ optional("--max-segment-intron", maxSegmentIntron) +
+ conditional(noSortBam, "--no-sort-bam") +
+ conditional(noConvertBam, "--no-convert-bam") +
+ conditional(keepFastaOrder, "--keep-fasta-order") +
+ conditional(allowPartialMapping, "--allow-partial-mapping") +
+ conditional(b2VeryFast, "--b2-very-fast") +
+ conditional(b2Fast, "--b2-fast") +
+ conditional(b2Sensitive, "--b2-sensitive") +
+ conditional(b2VerySensitive, "--b2-very-sensitive") +
+ optional("--b2-N", b2N) +
+ optional("--b2-L", b2L) +
+ optional("--b2-i", b2I) +
+ optional("--b2-n-ceil", b2NCeil) +
+ optional("--b2-gbar", b2Gbar) +
+ optional("--b2-mp", b2Mp) +
+ optional("--b2-np", b2Np) +
+ optional("--b2-rdg", b2Rdg) +
+ optional("--b2-rfg", b2Rfg) +
+ optional("--b2-score-min", b2ScoreMin) +
+ optional("--b2-D", b2D) +
+ optional("--b2-R", b2R) +
+ conditional(fusionSearch, "--fusion-search") +
+ optional("--fusion-anchor-length", fusionAnchorLength) +
+ optional("--fusion-min-dist", fusionMinDist) +
+ optional("--fusion-read-mismatches", fusionReadMismatches) +
+ optional("--fusion-multireads", fusionMultireads) +
+ optional("--fusion-multipairs", fusionMultipairs) +
+ optional("--fusion-ignore-chromosomes", fusionIgnoreChromosomes) +
+ conditional(fusionDoNotResolveConflicts, "--fusion-do-not-resolve-conflicts") +
+ optional("--rg-id", rgId) +
+ optional("--rg-sample", rgSample) +
+ optional("--rg-library", rgLibrary) +
+ optional("--rg-description", rgDescription) +
+ optional("--rg-platform-unit", rgPlatformUnit) +
+ optional("--rg-center", rgCenter) +
+ optional("--rg-date", rgDate) +
+ optional("--rg-platform", rgPlatform) +
+ required(bowtieIndex) +
required(R1.mkString(",")) +
optional(R2.mkString(","))
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 97b4c7413..c5c0a0446 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -48,21 +48,21 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var v: Boolean = config("v", default = true, freeVar = false)
var q: Boolean = config("q", default = false, freeVar = false)
var offline: Boolean = config("offline", default = false)
- var no_progress: Boolean = config("no_progress", default = false)
+ var noProgress: Boolean = config("no_progress", default = false)
var everything: Boolean = config("everything", default = false)
var force: Boolean = config("force", default = false)
- var no_stats: Boolean = config("no_stats", default = false)
- var stats_text: Boolean = config("stats_text", default = true)
+ var noStats: Boolean = config("no_stats", default = false)
+ var statsText: Boolean = config("stats_text", default = true)
var html: Boolean = config("html", default = false)
var cache: Boolean = config("cache", default = false)
var humdiv: Boolean = config("humdiv", default = false)
var regulatory: Boolean = config("regulatory", default = false)
- var cell_type: Boolean = config("cell_type", default = false)
+ var cellType: Boolean = config("cell_type", default = false)
var phased: Boolean = config("phased", default = false)
- var allele_number: Boolean = config("allele_number", default = false)
+ var alleleNumber: Boolean = config("allele_number", default = false)
var numbers: Boolean = config("numbers", default = false)
var domains: Boolean = config("domains", default = false)
- var no_escape: Boolean = config("no_escape", default = false)
+ var noEscape: Boolean = config("no_escape", default = false)
var hgvs: Boolean = config("hgvs", default = false)
var protein: Boolean = config("protein", default = false)
var symbol: Boolean = config("symbol", default = false)
@@ -71,50 +71,50 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var tsl: Boolean = config("tsl", default = false)
var canonical: Boolean = config("canonical", default = false)
var biotype: Boolean = config("biotype", default = false)
- var xref_refseq: Boolean = config("xref_refseq", default = false)
- var check_existing: Boolean = config("check_existing", default = false)
- var check_alleles: Boolean = config("check_alleles", default = false)
- var check_svs: Boolean = config("svs", default = false)
+ var xrefRefseq: Boolean = config("xref_refseq", default = false)
+ var checkExisting: Boolean = config("check_existing", default = false)
+ var checkAlleles: Boolean = config("check_alleles", default = false)
+ var checkSvs: Boolean = config("svs", default = false)
var gmaf: Boolean = config("gmaf", default = false)
- var maf_1kg: Boolean = config("maf_1kg", default = false)
- var maf_esp: Boolean = config("maf_esp", default = false)
- var old_map: Boolean = config("old_maf", default = false)
+ var maf1kg: Boolean = config("maf_1kg", default = false)
+ var mafEsp: Boolean = config("maf_esp", default = false)
+ var oldMap: Boolean = config("old_maf", default = false)
var pubmed: Boolean = config("pubmed", default = false)
var vcf: Boolean = config("vcf", default = true, freeVar = false)
var json: Boolean = config("json", default = false, freeVar = false)
var gvf: Boolean = config("gvf", default = false)
- var check_ref: Boolean = config("check_ref", default = false)
- var coding_only: Boolean = config("coding_only", default = false)
- var no_intergenic: Boolean = config("no_intergenic", default = false)
+ var checkRef: Boolean = config("check_ref", default = false)
+ var codingOnly: Boolean = config("coding_only", default = false)
+ var noIntergenic: Boolean = config("no_intergenic", default = false)
var pick: Boolean = config("pick", default = false)
- var pick_allele: Boolean = config("pick_allele", default = false)
- var flag_pick: Boolean = config("flag_pick", default = false)
- var flag_pick_allele: Boolean = config("flag_pick_allele", default = false)
- var per_gene: Boolean = config("per_gene", default = false)
- var most_severe: Boolean = config("most_severe", default = false)
+ var pickAllele: Boolean = config("pick_allele", default = false)
+ var flagPick: Boolean = config("flag_pick", default = false)
+ var flagPickAllele: Boolean = config("flag_pick_allele", default = false)
+ var perGene: Boolean = config("per_gene", default = false)
+ var mostSevere: Boolean = config("most_severe", default = false)
var summary: Boolean = config("summary", default = false)
- var filter_common: Boolean = config("filter_common", default = false)
- var check_frequency: Boolean = config("check_frequency", default = false)
- var allow_non_variant: Boolean = config("allow_non_variant", default = false)
+ var filterCommon: Boolean = config("filter_common", default = false)
+ var checkFrequency: Boolean = config("check_frequency", default = false)
+ var allowNonVariant: Boolean = config("allow_non_variant", default = false)
var database: Boolean = config("database", default = false)
var genomes: Boolean = config("genomes", default = false)
- var gencode_basic: Boolean = config("gencode_basic", default = false)
+ var gencodeBasic: Boolean = config("gencode_basic", default = false)
var refseq: Boolean = config("refseq", default = false)
var merged: Boolean = config("merged", default = false)
- var all_refseq: Boolean = config("all_refseq", default = false)
+ var allRefseq: Boolean = config("all_refseq", default = false)
var lrg: Boolean = config("lrg", default = false)
- var no_whole_genome: Boolean = config("no_whole_genome", default = false)
- var skip_db_check: Boolean = config("skip_db_check", default = false)
+ var noWholeGenome: Boolean = config("no_whole_genome", default = false)
+ var skibDbCheck: Boolean = config("skip_db_check", default = false)
// Textual args
- var vep_config: Option[String] = config("config", freeVar = false)
+ var vepConfig: Option[String] = config("config", freeVar = false)
var species: Option[String] = config("species", freeVar = false)
var assembly: Option[String] = config("assembly")
var format: Option[String] = config("format")
var dir: Option[String] = config("dir")
- var dir_cache: Option[String] = config("dir_cache")
- var dir_plugins: Option[String] = config("dir_plugins")
+ var dirCache: Option[String] = config("dir_cache")
+ var dirPlugins: Option[String] = config("dir_plugins")
var fasta: Option[String] = config("fasta")
var sift: Option[String] = config("sift")
var polyphen: Option[String] = config("polyphen")
@@ -125,10 +125,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var convert: Option[String] = config("convert")
var terms: Option[String] = config("terms")
var chr: Option[String] = config("chr")
- var pick_order: Option[String] = config("pick_order")
- var freq_pop: Option[String] = config("check_pop")
- var freq_gt_lt: Option[String] = config("freq_gt_lt")
- var freq_filter: Option[String] = config("freq_filter")
+ var pickOrder: Option[String] = config("pick_order")
+ var freqPop: Option[String] = config("check_pop")
+ var freqGtLt: Option[String] = config("freq_gt_lt")
+ var freqFilter: Option[String] = config("freq_filter")
var filter: Option[String] = config("filter")
var host: Option[String] = config("host")
var user: Option[String] = config("user")
@@ -136,15 +136,15 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var registry: Option[String] = config("registry")
var build: Option[String] = config("build")
var compress: Option[String] = config("compress")
- var cache_region_size: Option[String] = config("cache_region_size")
+ var cacheRegionSize: Option[String] = config("cache_region_size")
// Numeric args
override def defaultThreads: Int = config("fork", default = 2)
- var cache_version: Option[Int] = config("cache_version")
- var freq_freq: Option[Float] = config("freq_freq")
+ var cacheVersion: Option[Int] = config("cache_version")
+ var freqFreq: Option[Float] = config("freq_freq")
var port: Option[Int] = config("port")
- var db_version: Option[Int] = config("db_version")
- var buffer_size: Option[Int] = config("buffer_size")
+ var dbVersion: Option[Int] = config("db_version")
+ var bufferSize: Option[Int] = config("buffer_size")
// ought to be a flag, but is BUG in VEP; becomes numeric ("1" is true)
var failed: Option[Int] = config("failed")
@@ -165,21 +165,21 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
conditional(v, "-v") +
conditional(q, "-q") +
conditional(offline, "--offline") +
- conditional(no_progress, "--no_progress") +
+ conditional(noProgress, "--no_progress") +
conditional(everything, "--everything") +
conditional(force, "--force_overwrite") +
- conditional(no_stats, "--no_stats") +
- conditional(stats_text, "--stats_text") +
+ conditional(noStats, "--no_stats") +
+ conditional(statsText, "--stats_text") +
conditional(html, "--html") +
conditional(cache, "--cache") +
conditional(humdiv, "--humdiv") +
conditional(regulatory, "--regulatory") +
- conditional(cell_type, "--cel_type") +
+ conditional(cellType, "--cel_type") +
conditional(phased, "--phased") +
- conditional(allele_number, "--allele_number") +
+ conditional(alleleNumber, "--allele_number") +
conditional(numbers, "--numbers") +
conditional(domains, "--domains") +
- conditional(no_escape, "--no_escape") +
+ conditional(noEscape, "--no_escape") +
conditional(hgvs, "--hgvs") +
conditional(protein, "--protein") +
conditional(symbol, "--symbol") +
@@ -188,46 +188,46 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
conditional(tsl, "--tsl") +
conditional(canonical, "--canonical") +
conditional(biotype, "--biotype") +
- conditional(xref_refseq, "--xref_refseq") +
- conditional(check_existing, "--check_existing") +
- conditional(check_alleles, "--check_alleles") +
- conditional(check_svs, "--check_svs") +
+ conditional(xrefRefseq, "--xref_refseq") +
+ conditional(checkExisting, "--check_existing") +
+ conditional(checkAlleles, "--check_alleles") +
+ conditional(checkSvs, "--check_svs") +
conditional(gmaf, "--gmaf") +
- conditional(maf_1kg, "--maf_1kg") +
- conditional(maf_esp, "--maf_esp") +
+ conditional(maf1kg, "--maf_1kg") +
+ conditional(mafEsp, "--maf_esp") +
conditional(pubmed, "--pubmed") +
conditional(vcf, "--vcf") +
conditional(json, "--json") +
conditional(gvf, "--gvf") +
- conditional(check_ref, "--check_ref") +
- conditional(coding_only, "--coding_only") +
- conditional(no_intergenic, "--no_intergenic") +
+ conditional(checkRef, "--check_ref") +
+ conditional(codingOnly, "--coding_only") +
+ conditional(noIntergenic, "--no_intergenic") +
conditional(pick, "--pick") +
- conditional(pick_allele, "--pick_allele") +
- conditional(flag_pick, "--flag_pick") +
- conditional(flag_pick_allele, "--flag_pick_allele") +
- conditional(per_gene, "--per_gene") +
- conditional(most_severe, "--most_severe") +
+ conditional(pickAllele, "--pick_allele") +
+ conditional(flagPick, "--flag_pick") +
+ conditional(flagPickAllele, "--flag_pick_allele") +
+ conditional(perGene, "--per_gene") +
+ conditional(mostSevere, "--most_severe") +
conditional(summary, "--summary") +
- conditional(filter_common, "--filter_common") +
- conditional(check_frequency, "--check_frequency") +
- conditional(allow_non_variant, "--allow_non_variant") +
+ conditional(filterCommon, "--filter_common") +
+ conditional(checkFrequency, "--check_frequency") +
+ conditional(allowNonVariant, "--allow_non_variant") +
conditional(database, "--database") +
conditional(genomes, "--genomes") +
- conditional(gencode_basic, "--gencode_basic") +
+ conditional(gencodeBasic, "--gencode_basic") +
conditional(refseq, "--refseq") +
conditional(merged, "--merged") +
- conditional(all_refseq, "--all_refseq") +
+ conditional(allRefseq, "--all_refseq") +
conditional(lrg, "--lrg") +
- conditional(no_whole_genome, "--no_whole_genome") +
- conditional(skip_db_check, "--skip_db_check") +
- optional("--config", vep_config) +
+ conditional(noWholeGenome, "--no_whole_genome") +
+ conditional(skibDbCheck, "--skip_db_check") +
+ optional("--config", vepConfig) +
optional("--species", species) +
optional("--assembly", assembly) +
optional("--format", format) +
optional("--dir", dir) +
- optional("--dir_cache", dir_cache) +
- optional("--dir_plugins", dir_plugins) +
+ optional("--dir_cache", dirCache) +
+ optional("--dir_plugins", dirPlugins) +
optional("--fasta", fasta) +
optional("--sift", sift) +
optional("--polyphen", polyphen) +
@@ -238,10 +238,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--convert", convert) +
optional("--terms", terms) +
optional("--chr", chr) +
- optional("--pick_order", pick_order) +
- optional("--freq_pop", freq_pop) +
- optional("--freq_gt_lt", freq_gt_lt) +
- optional("--freq_filter", freq_filter) +
+ optional("--pick_order", pickOrder) +
+ optional("--freq_pop", freqPop) +
+ optional("--freq_gt_lt", freqGtLt) +
+ optional("--freq_filter", freqFilter) +
optional("--filter", filter) +
optional("--host", host) +
optional("--user", user) +
@@ -249,19 +249,19 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--registry", registry) +
optional("--build", build) +
optional("--compress", compress) +
- optional("--cache_region_size", cache_region_size) +
+ optional("--cache_region_size", cacheRegionSize) +
optional("--fork", threads) +
- optional("--cache_version", cache_version) +
- optional("--freq_freq", freq_freq) +
+ optional("--cache_version", cacheVersion) +
+ optional("--freq_freq", freqFreq) +
optional("--port", port) +
- optional("--db_version", db_version) +
- optional("--buffer_size", buffer_size) +
+ optional("--db_version", dbVersion) +
+ optional("--buffer_size", bufferSize) +
optional("--failed", failed)
def summaryFiles: Map[String, File] = Map()
def summaryStats: Map[String, Any] = {
- if (stats_text) {
+ if (statsText) {
val stats_file: File = new File(output.getAbsolutePath + "_summary.txt")
parseStatsFile(stats_file)
} else {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
index 429c65b98..92abaded5 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
@@ -46,7 +46,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
override def defaultThreads = 8
var sam: Boolean = config("sam", default = false)
- var sam_RG: Option[String] = config("sam-RG")
+ var samRg: Option[String] = config("sam-RG")
var seedlen: Option[Int] = config("seedlen")
var seedmms: Option[Int] = config("seedmms")
var k: Option[Int] = config("k")
@@ -80,7 +80,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
conditional(largeIndex, "--large-index") +
conditional(best, "--best") +
conditional(strata, "--strata") +
- optional("--sam-RG", sam_RG) +
+ optional("--sam-RG", samRg) +
optional("--seedlen", seedlen) +
optional("--seedmms", seedmms) +
optional("-k", k) +
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
index 793fd7d15..2ebce9331 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
@@ -45,20 +45,20 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var trim3: Option[Int] = config("trim3")
var phred33: Boolean = config("phred33", default = false)
var phred64: Boolean = config("phred64", default = false)
- var int_quals: Boolean = config("int_quals", default = false)
+ var intQuals: Boolean = config("int_quals", default = false)
/* Alignment options */
var N: Option[Int] = config("N")
var L: Option[Int] = config("L")
var i: Option[String] = config("i")
- var n_ceil: Option[String] = config("n_ceil")
+ var nCeil: Option[String] = config("n_ceil")
var dpad: Option[Int] = config("dpad")
var gbar: Option[Int] = config("gbar")
- var ignore_quals: Boolean = config("ignore_quals", default = false)
+ var ignoreQuals: Boolean = config("ignore_quals", default = false)
var nofw: Boolean = config("nofw", default = false)
var norc: Boolean = config("norc", default = false)
- var no_1mm_upfront: Boolean = config("no_1mm_upfront", default = false)
- var end_to_end: Boolean = config("end_to_end", default = false)
+ var no1MmUpfront: Boolean = config("no_1mm_upfront", default = false)
+ var endToEnd: Boolean = config("end_to_end", default = false)
var local: Boolean = config("local", default = false)
/* Scoring */
@@ -67,7 +67,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var np: Option[Int] = config("np")
var rdg: Option[String] = config("rdg")
var rfg: Option[String] = config("rfg")
- var score_min: Option[String] = config("score_min")
+ var scoreMin: Option[String] = config("score_min")
/* Reporting */
var k: Option[Int] = config("k")
@@ -83,52 +83,52 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var fr: Boolean = config("fr", default = false)
var rf: Boolean = config("rf", default = false)
var ff: Boolean = config("ff", default = false)
- var no_mixed: Boolean = config("no_mixed", default = false)
- var no_discordant: Boolean = config("no_discordant", default = false)
- var no_dovetail: Boolean = config("no_dovetail", default = false)
- var no_contain: Boolean = config("no_contain", default = false)
- var no_overlap: Boolean = config("no_overlap", default = false)
+ var noMixed: Boolean = config("no_mixed", default = false)
+ var noDiscordant: Boolean = config("no_discordant", default = false)
+ var noDovetail: Boolean = config("no_dovetail", default = false)
+ var noContain: Boolean = config("no_contain", default = false)
+ var noOverlap: Boolean = config("no_overlap", default = false)
/* Output */
var time: Boolean = config("no_overlap", default = false)
var un: Option[String] = config("un")
var al: Option[String] = config("al")
- var un_conc: Option[String] = config("un_conc")
- var al_conc: Option[String] = config("al_conc")
+ var unConc: Option[String] = config("un_conc")
+ var alConc: Option[String] = config("al_conc")
- var un_gz: Option[String] = config("un_gz")
- var al_gz: Option[String] = config("al_gz")
- var un_conc_gz: Option[String] = config("un_conc_gz")
- var al_conc_gz: Option[String] = config("al_conc_gz")
+ var unGz: Option[String] = config("un_gz")
+ var alGz: Option[String] = config("al_gz")
+ var unConcGz: Option[String] = config("un_conc_gz")
+ var alConcGz: Option[String] = config("al_conc_gz")
- var un_bz2: Option[String] = config("un_bz2")
- var al_bz2: Option[String] = config("al_bz2")
- var un_conc_bz2: Option[String] = config("un_conc_bz2")
- var al_conc_bz2: Option[String] = config("al_conc_bz2")
+ var unBz2: Option[String] = config("un_bz2")
+ var alBz2: Option[String] = config("al_bz2")
+ var unConcBz2: Option[String] = config("un_conc_bz2")
+ var alConcBz2: Option[String] = config("al_conc_bz2")
var quiet: Boolean = config("quiet", default = false)
- var met_file: Option[String] = config("met_file")
- var met_stderr: Boolean = config("met_stderr", default = false)
+ var metFile: Option[String] = config("met_file")
+ var metStderr: Boolean = config("met_stderr", default = false)
var met: Option[Int] = config("met")
- var no_unal: Boolean = config("no_unal", default = false)
- var no_head: Boolean = config("no_head", default = false)
- var no_sq: Boolean = config("no_sq", default = false)
+ var noUnal: Boolean = config("no_unal", default = false)
+ var noHead: Boolean = config("no_head", default = false)
+ var noSq: Boolean = config("no_sq", default = false)
- var rg_id: Option[String] = config("rg_id")
+ var rgId: Option[String] = config("rg_id")
var rg: List[String] = config("rg", default = Nil)
- var omit_sec_seq: Boolean = config("omit_sec_seq", default = false)
+ var omitSecSeq: Boolean = config("omit_sec_seq", default = false)
/* Performance */
var reorder: Boolean = config("reorder", default = false)
var mm: Boolean = config("mm", default = false)
/* Other */
- var qc_filter: Boolean = config("qc_filter", default = false)
+ var qcFilter: Boolean = config("qc_filter", default = false)
var seed: Option[Int] = config("seed")
- var non_deterministic: Boolean = config("non_deterministic", default = false)
+ var nonDeterministic: Boolean = config("non_deterministic", default = false)
override def beforeGraph() {
super.beforeGraph()
@@ -153,19 +153,19 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
optional("--trim5", trim5) +
conditional(phred33, "--phred33") +
conditional(phred64, "--phred64") +
- conditional(int_quals, "--int-quals") +
+ conditional(intQuals, "--int-quals") +
/* Alignment options */
optional("-N", N) +
optional("-L", L) +
optional("-i", i) +
- optional("--n-ceil", n_ceil) +
+ optional("--n-ceil", nCeil) +
optional("--dpad", dpad) +
optional("--gbar", gbar) +
- conditional(ignore_quals, "--ignore-quals") +
+ conditional(ignoreQuals, "--ignore-quals") +
conditional(nofw, "--nofw") +
conditional(norc, "--norc") +
- conditional(no_1mm_upfront, "--no-1mm-upfront") +
- conditional(end_to_end, "--end-to-end") +
+ conditional(no1MmUpfront, "--no-1mm-upfront") +
+ conditional(endToEnd, "--end-to-end") +
conditional(local, "--local") +
/* Scoring */
optional("--ma", ma) +
@@ -173,7 +173,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
optional("--np", np) +
optional("--rdg", rdg) +
optional("--rfg", rfg) +
- optional("--score-min", score_min) +
+ optional("--score-min", scoreMin) +
/* Reporting */
optional("-k", k) +
optional("--all", all) +
@@ -186,43 +186,43 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
conditional(fr, "--fr") +
conditional(rf, "--rf") +
conditional(ff, "--ff") +
- conditional(no_mixed, "--no-mixed") +
- conditional(no_discordant, "--no-discordant") +
- conditional(no_dovetail, "--no-dovetail") +
- conditional(no_contain, "--no-contain") +
- conditional(no_overlap, "--no-overlap") +
+ conditional(noMixed, "--no-mixed") +
+ conditional(noDiscordant, "--no-discordant") +
+ conditional(noDovetail, "--no-dovetail") +
+ conditional(noContain, "--no-contain") +
+ conditional(noOverlap, "--no-overlap") +
/* Output */
conditional(time, "--time") +
optional("--un", un) +
optional("--al", al) +
- optional("--un-conc", un_conc) +
- optional("--al-conc", al_conc) +
- optional("--un-gz", un_gz) +
- optional("--al-gz", al_gz) +
- optional("--un-conc-gz", un_conc_gz) +
- optional("--al-conc-gz", al_conc_gz) +
- optional("--un-bz2", un_bz2) +
- optional("--al-bz2", al_bz2) +
- optional("--un-conc-bz2", un_conc_bz2) +
- optional("--al-conc-bz2", al_conc_bz2) +
+ optional("--un-conc", unConc) +
+ optional("--al-conc", alConc) +
+ optional("--un-gz", unGz) +
+ optional("--al-gz", alGz) +
+ optional("--un-conc-gz", unConcGz) +
+ optional("--al-conc-gz", alConcGz) +
+ optional("--un-bz2", unBz2) +
+ optional("--al-bz2", alBz2) +
+ optional("--un-conc-bz2", unConcBz2) +
+ optional("--al-conc-bz2", alConcBz2) +
conditional(quiet, "--quiet") +
- optional("--met-file", met_file) +
- conditional(met_stderr, "--met-stderr") +
+ optional("--met-file", metFile) +
+ conditional(metStderr, "--met-stderr") +
optional("--met", met) +
- conditional(no_unal, "--no-unal") +
- conditional(no_head, "--no-head") +
- conditional(no_sq, "--no-sq") +
- optional("--rg-id", rg_id) +
+ conditional(noUnal, "--no-unal") +
+ conditional(noHead, "--no-head") +
+ conditional(noSq, "--no-sq") +
+ optional("--rg-id", rgId) +
repeat("--rg", rg) +
- conditional(omit_sec_seq, "--omit-sec-seq") +
+ conditional(omitSecSeq, "--omit-sec-seq") +
/* Performance */
optional("--threads", threads) +
conditional(reorder, "--reorder") +
conditional(mm, "--mm") +
/* Other */
- conditional(qc_filter, "--qc-filter") +
+ conditional(qcFilter, "--qc-filter") +
optional("--seed", seed) +
- conditional(non_deterministic, "--non-deterministic") +
+ conditional(nonDeterministic, "--non-deterministic") +
/* Required */
required("-x", bowtieIndex) +
(R2 match {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
index 2b310aaf8..7986c8374 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
@@ -30,26 +30,26 @@ class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunctio
@Output(doc = "Output File")
var output: File = _
- var min_mq: Option[Int] = config("min_mq", default = 20) // minimum of MQ to consider for taking read into histogram
- var use_mq: Boolean = config("use_mq", default = false)
- var min_insertsize: Option[Int] = config("min_insertsize")
- var solid_data: Boolean = config("solid", default = false)
- var sd_cutoff: Option[Int] = config("sd_cutoff") // Cutoff in unit of standard deviation [4]
+ var minMq: Option[Int] = config("min_mq", default = 20) // minimum of MQ to consider for taking read into histogram
+ var useMq: Boolean = config("use_mq", default = false)
+ var minInsertsize: Option[Int] = config("min_insertsize")
+ var solidData: Boolean = config("solid", default = false)
+ var sdCutoff: Option[Int] = config("sd_cutoff") // Cutoff in unit of standard deviation [4]
// we set this to a higher number to avoid biases in small numbers in sorted bams
- var min_observations: Option[Int] = config("min_observations") // Number of observation required to estimate mean and s.d. insert size [10_000]
- var coefvar_cutoff: Option[Int] = config("coef_cutoff") // Cutoff on coefficients of variation [1]
- var histogram_bins: Option[Int] = config("histogram_bins") // Number of bins in the histogram [50]
+ var minObservations: Option[Int] = config("min_observations") // Number of observation required to estimate mean and s.d. insert size [10_000]
+ var coefvarCutoff: Option[Int] = config("coef_cutoff") // Cutoff on coefficients of variation [1]
+ var histogramBins: Option[Int] = config("histogram_bins") // Number of bins in the histogram [50]
def cmdLine = required(executable) +
- optional("-q", min_mq) +
- conditional(use_mq, "-m") +
- optional("-s", min_insertsize) +
- conditional(solid_data, "-s") +
- optional("-c", sd_cutoff) +
- optional("-n", min_observations) +
- optional("-v", coefvar_cutoff) +
- optional("-b", histogram_bins) +
+ optional("-q", minMq) +
+ conditional(useMq, "-m") +
+ optional("-s", minInsertsize) +
+ conditional(solidData, "-s") +
+ optional("-c", sdCutoff) +
+ optional("-n", minObservations) +
+ optional("-v", coefvarCutoff) +
+ optional("-b", histogramBins) +
required(input) + " 1> " + required(output)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
index 5f517d7b3..f241c576e 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
@@ -24,7 +24,7 @@ abstract class Conifer extends PythonCommandLineFunction with Version {
setPythonScript(config("script", default = "conifer"))
def versionRegex = """(.*)""".r
override def versionExitcode = List(0)
- def versionCommand = executable + " " + python_script + " --version"
+ def versionCommand = executable + " " + pythonScript + " --version"
override def defaultCoreMemory = 5.0
override def defaultThreads = 1
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
index 284d0e059..40790f0ac 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
@@ -36,7 +36,7 @@ class ConiferAnalyze(val root: Configurable) extends Conifer {
var svd: Option[Int] = config("svd", default = 1)
@Argument(doc = "Minimum population median RPKM per probe", required = false)
- var min_rpkm: Option[Double] = config("min_rpkm")
+ var minRpkm: Option[Double] = config("min_rpkm")
override def cmdLine = super.cmdLine +
" analyze " +
@@ -44,5 +44,5 @@ class ConiferAnalyze(val root: Configurable) extends Conifer {
" --rpkm_dir" + required(rpkmDir) +
" --output" + required(output) +
optional("--svd", svd) +
- optional("--min_rpkm", min_rpkm)
+ optional("--min_rpkm", minRpkm)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
index 7b92be3b1..d8059551c 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala
@@ -53,7 +53,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
var db: String = config("db")
/** whether to use a suffix array, which will give increased speed */
- var use_sarray: Option[Int] = config("use_sarray")
+ var useSarray: Option[Int] = config("use_sarray")
/** kmer size to use in genome database (allowed values: 16 or less) */
var kmer: Option[Int] = config("kmer")
@@ -65,28 +65,28 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
var part: Option[String] = config("part")
/** size of input buffer (program reads this many sequences at a time)*/
- var input_buffer_size: Option[Int] = config("input_buffer_size")
+ var inputBufferSize: Option[Int] = config("input_buffer_size")
/** amount of barcode to remove from start of read */
- var barcode_length: Option[Int] = config("barcode_length")
+ var barcodeLength: Option[Int] = config("barcode_length")
/** orientation of paired-end reads */
var orientation: Option[String] = config("orientation")
/** starting position of identifier in fastq header, space-delimited (>= 1) */
- var fastq_id_start: Option[Int] = config("fastq_id_start")
+ var fastqIdStart: Option[Int] = config("fastq_id_start")
/** ending position of identifier in fastq header, space-delimited (>= 1) */
- var fastq_id_end: Option[Int] = config("fastq_id_end")
+ var fastqIdEnd: Option[Int] = config("fastq_id_end")
/** when multiple fastq files are provided on the command line, gsnap assumes */
- var force_single_end: Boolean = config("force_single_end", default = false)
+ var forceSingleEnd: Boolean = config("force_single_end", default = false)
/** skips reads marked by the illumina chastity program. expecting a string */
- var filter_chastity: Option[String] = config("filter_chastity")
+ var filterChastity: Option[String] = config("filter_chastity")
/** allows accession names of reads to mismatch in paired-end files */
- var allow_pe_name_mismatch: Boolean = config("allow_pe_name_mismatch", default = false)
+ var allowPeNameMismatch: Boolean = config("allow_pe_name_mismatch", default = false)
/** uncompress gzipped input files */
var gunzip: Boolean = config("gunzip", default = false)
@@ -98,61 +98,61 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
var batch: Option[Int] = config("batch")
/** whether to expand the genomic offsets index */
- var expand_offsets: Option[Int] = config("expand_offsets")
+ var expandOffsets: Option[Int] = config("expand_offsets")
/** maximum number of mismatches allowed (if not specified, then */
- var max_mismatches: Option[Float] = config("max_mismatches")
+ var maxMismatches: Option[Float] = config("max_mismatches")
/** whether to count unknown (n) characters in the query as a mismatch */
- var query_unk_mismatch: Option[Int] = config("query_unk_mismatch")
+ var queryUnkMismatch: Option[Int] = config("query_unk_mismatch")
/** whether to count unknown (n) characters in the genome as a mismatch */
- var genome_unk_mismatch: Option[Int] = config("genome_unk_mismatch")
+ var genomeUnkMismatch: Option[Int] = config("genome_unk_mismatch")
/** maximum number of alignments to find (default 1000) */
var maxsearch: Option[Int] = config("maxsearch")
/** threshold for computing a terminal alignment (from one end of the */
- var terminal_threshold: Option[Int] = config("terminal_threshold")
+ var terminalThreshold: Option[Int] = config("terminal_threshold")
/** threshold alignment length in bp for a terminal alignment result to be printed (in bp) */
- var terminal_output_minlength: Option[Int] = config("terminal_output_minlength")
+ var terminalOutputMinlength: Option[Int] = config("terminal_output_minlength")
/** penalty for an indel (default 2) */
- var indel_penalty: Option[Int] = config("indel_penalty")
+ var indelPenalty: Option[Int] = config("indel_penalty")
/** minimum length at end required for indel alignments (default 4) */
- var indel_endlength: Option[Int] = config("indel_endlength")
+ var indelEndlength: Option[Int] = config("indel_endlength")
/** maximum number of middle insertions allowed (default 9) */
- var max_middle_insertions: Option[Int] = config("max_middle_insertions")
+ var maxMiddleInsertions: Option[Int] = config("max_middle_insertions")
/** maximum number of middle deletions allowed (default 30) */
- var max_middle_deletions: Option[Int] = config("max_middle_deletions")
+ var maxMiddleDeletions: Option[Int] = config("max_middle_deletions")
/** maximum number of end insertions allowed (default 3) */
- var max_end_insertions: Option[Int] = config("max_end_insertions")
+ var maxEndInsertions: Option[Int] = config("max_end_insertions")
/** maximum number of end deletions allowed (default 6) */
- var max_end_deletions: Option[Int] = config("max_end_deletions")
+ var maxEndDeletions: Option[Int] = config("max_end_deletions")
/** report suboptimal hits beyond best hit (default 0) */
- var suboptimal_levels: Option[Int] = config("suboptimal_levels")
+ var suboptimalLevels: Option[Int] = config("suboptimal_levels")
/** method for removing adapters from reads. currently allowed values: off, paired */
- var adapter_strip: Option[String] = config("adapter_strip")
+ var adapterStrip: Option[String] = config("adapter_strip")
/** score to use for mismatches when trimming at ends (default is -3; */
- var trim_mismatch_score: Option[Int] = config("trim_mismatch_score")
+ var trimMismatchScore: Option[Int] = config("trim_mismatch_score")
/** score to use for indels when trimming at ends (default is -4; */
- var trim_indel_score: Option[Int] = config("trim_indel_score")
+ var trimIndelScore: Option[Int] = config("trim_indel_score")
/** directory for snps index files (created using snpindex) (default is */
var snpsdir: Option[String] = config("snpsdir")
/** use database containing known snps (in <string>.iit, built */
- var use_snps: Option[String] = config("use_snps")
+ var useSnps: Option[String] = config("use_snps")
/** directory for methylcytosine index files (created using cmetindex) */
var cmetdir: Option[String] = config("cmetdir")
@@ -167,166 +167,166 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
var tallydir: Option[String] = config("tallydir")
/** use this tally iit file to resolve concordant multiple results */
- var use_tally: Option[String] = config("use_tally")
+ var useTally: Option[String] = config("use_tally")
/** directory for runlength iit file to resolve concordant multiple results (default is */
- var runlengthdir: Option[String] = config("runlengthdir")
+ var runLengthDir: Option[String] = config("runlengthdir")
/** use this runlength iit file to resolve concordant multiple results */
- var use_runlength: Option[String] = config("use_runlength")
+ var useRunlength: Option[String] = config("use_runlength")
/** cases to use gmap for complex alignments containing multiple splices or indels */
- var gmap_mode: Option[String] = config("gmap_mode")
+ var gmapMode: Option[String] = config("gmap_mode")
/** try gmap pairsearch on nearby genomic regions if best score (the total */
- var trigger_score_for_gmap: Option[Int] = config("trigger_score_for_gmap")
+ var triggerScoreForGmap: Option[Int] = config("trigger_score_for_gmap")
/** keep gmap hit only if it has this many consecutive matches (default 20) */
- var gmap_min_match_length: Option[Int] = config("gmap_min_match_length")
+ var gmapMinMatchLength: Option[Int] = config("gmap_min_match_length")
/** extra mismatch/indel score allowed for gmap alignments (default 3) */
- var gmap_allowance: Option[Int] = config("gmap_allowance")
+ var gmapAllowance: Option[Int] = config("gmap_allowance")
/** perform gmap pairsearch on nearby genomic regions up to this many */
- var max_gmap_pairsearch: Option[Int] = config("max_gmap_pairsearch")
+ var maxGmapPairsearch: Option[Int] = config("max_gmap_pairsearch")
/** perform gmap terminal on nearby genomic regions up to this many */
- var max_gmap_terminal: Option[Int] = config("max_gmap_terminal")
+ var maxGmapTerminal: Option[Int] = config("max_gmap_terminal")
/** perform gmap improvement on nearby genomic regions up to this many */
- var max_gmap_improvement: Option[Int] = config("max_gmap_improvement")
+ var maxGmapImprovement: Option[Int] = config("max_gmap_improvement")
/** allow microexons only if one of the splice site probabilities is */
- var microexon_spliceprob: Option[Float] = config("microexon_spliceprob")
+ var microExonSpliceprob: Option[Float] = config("microexon_spliceprob")
/** look for novel splicing (0=no (default), 1=yes) */
- var novelsplicing: Option[Int] = config("novelsplicing")
+ var novelSplicing: Option[Int] = config("novelsplicing")
/** directory for splicing involving known sites or known introns, */
- var splicingdir: Option[String] = config("splicingdir")
+ var splicingDir: Option[String] = config("splicingdir")
/** look for splicing involving known sites or known introns */
- var use_splicing: Option[String] = config("use_splicing")
+ var useSplicing: Option[String] = config("use_splicing")
/** for ambiguous known splicing at ends of the read, do not clip at the */
- var ambig_splice_noclip: Boolean = config("ambig_splice_noclip", default = false)
+ var ambigSpliceNoclip: Boolean = config("ambig_splice_noclip", default = false)
/** definition of local novel splicing event (default 200000) */
- var localsplicedist: Option[Int] = config("localsplicedist")
+ var localSpliceDist: Option[Int] = config("localsplicedist")
/** distance to look for novel splices at the ends of reads (default 50000) */
- var novelend_splicedist: Option[Int] = config("novelend_splicedist")
+ var novelEndSplicedist: Option[Int] = config("novelend_splicedist")
/** penalty for a local splice (default 0). counts against mismatches allowed */
- var local_splice_penalty: Option[Int] = config("local_splice_penalty")
+ var localSplicePenalty: Option[Int] = config("local_splice_penalty")
/** penalty for a distant splice (default 1). a distant splice is one where */
- var distant_splice_penalty: Option[Int] = config("distant_splice_penalty")
+ var distantSplicePenalty: Option[Int] = config("distant_splice_penalty")
/** minimum length at end required for distant spliced alignments (default 20, min */
- var distant_splice_endlength: Option[Int] = config("distant_splice_endlength")
+ var distantSpliceEndlength: Option[Int] = config("distant_splice_endlength")
/** minimum length at end required for short-end spliced alignments (default 2, */
- var shortend_splice_endlength: Option[Int] = config("shortend_splice_endlength")
+ var shortendSpliceEndlength: Option[Int] = config("shortend_splice_endlength")
/** minimum identity at end required for distant spliced alignments (default 0.95) */
- var distant_splice_identity: Option[Float] = config("distant_splice_identity")
+ var distantSpliceIdentity: Option[Float] = config("distant_splice_identity")
/** (not currently implemented) */
- var antistranded_penalty: Option[Int] = config("antistranded_penalty")
+ var antiStrandedPenalty: Option[Int] = config("antistranded_penalty")
/** report distant splices on the same chromosome as a single splice, if possible */
- var merge_distant_samechr: Boolean = config("merge_distant_samechr", default = false)
+ var mergeDistantSamechr: Boolean = config("merge_distant_samechr", default = false)
/** max total genomic length for dna-seq paired reads, or other reads */
- var pairmax_dna: Option[Int] = config("pairmax_dna")
+ var pairmaxDna: Option[Int] = config("pairmax_dna")
/** max total genomic length for rna-seq paired reads, or other reads */
- var pairmax_rna: Option[Int] = config("pairmax_rna")
+ var pairmaxRna: Option[Int] = config("pairmax_rna")
/** expected paired-end length, used for calling splices in medial part of */
- var pairexpect: Option[Int] = config("pairexpect")
+ var pairExpect: Option[Int] = config("pairexpect")
/** allowable deviation from expected paired-end length, used for */
- var pairdev: Option[Int] = config("pairdev")
+ var pairDev: Option[Int] = config("pairdev")
/** protocol for input quality scores. allowed values: */
- var quality_protocol: Option[String] = config("quality_protocol")
+ var qualityProtocol: Option[String] = config("quality_protocol")
/** fastq quality scores are zero at this ascii value */
- var quality_zero_score: Option[Int] = config("quality_zero_score")
+ var qualityZeroScore: Option[Int] = config("quality_zero_score")
/** shift fastq quality scores by this amount in output */
- var quality_print_shift: Option[Int] = config("quality_print_shift")
+ var qualityPrintShift: Option[Int] = config("quality_print_shift")
/** maximum number of paths to print (default 100) */
var npaths: Option[Int] = config("npaths")
/** if more than maximum number of paths are found, */
- var quiet_if_excessive: Boolean = config("quiet_if_excessive", default = false)
+ var quietIfExcessive: Boolean = config("quiet_if_excessive", default = false)
/** print output in same order as input (relevant */
var ordered: Boolean = config("ordered", default = false)
/** for gsnap output in snp-tolerant alignment, shows all differences */
- var show_refdiff: Boolean = config("show_refdiff", default = false)
+ var showRefdiff: Boolean = config("show_refdiff", default = false)
/** for paired-end reads whose alignments overlap, clip the overlapping region */
- var clip_overlap: Boolean = config("clip_overlap", default = false)
+ var clipOverlap: Boolean = config("clip_overlap", default = false)
/** print detailed information about snps in reads (works only if -v also selected) */
- var print_snps: Boolean = config("print_snps", default = false)
+ var printSnps: Boolean = config("print_snps", default = false)
/** print only failed alignments, those with no results */
- var failsonly: Boolean = config("failsonly", default = false)
+ var failsOnly: Boolean = config("failsonly", default = false)
/** exclude printing of failed alignments */
- var nofails: Boolean = config("nofails", default = false)
+ var noFails: Boolean = config("nofails", default = false)
/** print completely failed alignments as input fasta or fastq format */
- var fails_as_input: Boolean = config("fails_as_input", default = false)
+ var failsAsInput: Boolean = config("fails_as_input", default = false)
/** another format type, other than default */
var format: Option[String] = config("format")
/** basename for multiple-file output, separately for nomapping, */
- var split_output: Option[String] = config("split_output")
+ var splitOutput: Option[String] = config("split_output")
/** when --split-output is given, this flag will append output to the */
- var append_output: Boolean = config("append_output", default = false)
+ var appendOutput: Boolean = config("append_output", default = false)
/** buffer size, in queries, for output thread (default 1000). when the number */
- var output_buffer_size: Option[Int] = config("output_buffer_size")
+ var outputBufferSize: Option[Int] = config("output_buffer_size")
/** do not print headers beginning with '@' */
- var no_sam_headers: Boolean = config("no_sam_headers", default = false)
+ var noSamHeaders: Boolean = config("no_sam_headers", default = false)
/** print headers only for this batch, as specified by -q */
- var sam_headers_batch: Option[Int] = config("sam_headers_batch")
+ var samHeadersBatch: Option[Int] = config("sam_headers_batch")
/** insert 0m in cigar between adjacent insertions and deletions */
- var sam_use_0M: Boolean = config("sam_use_0M", default = false)
+ var samUse0M: Boolean = config("sam_use_0M", default = false)
/** allows multiple alignments to be marked as primary if they */
- var sam_multiple_primaries: Boolean = config("sam_multiple_primaries", default = false)
+ var samMultiplePrimaries: Boolean = config("sam_multiple_primaries", default = false)
/** for rna-seq alignments, disallows xs:a:? when the sense direction */
- var force_xs_dir: Boolean = config("force_xs_dir", default = false)
+ var forceXsDir: Boolean = config("force_xs_dir", default = false)
/** in md string, when known snps are given by the -v flag, */
- var md_lowercase_snp: Boolean = config("md_lowercase_snp", default = false)
+ var mdLowercaseSnp: Boolean = config("md_lowercase_snp", default = false)
/** value to put into read-group id (rg-id) field */
- var read_group_id: Option[String] = config("read_group_id")
+ var readGroupId: Option[String] = config("read_group_id")
/** value to put into read-group name (rg-sm) field */
- var read_group_name: Option[String] = config("read_group_name")
+ var readGroupName: Option[String] = config("read_group_name")
/** value to put into read-group library (rg-lb) field */
- var read_group_library: Option[String] = config("read_group_library")
+ var readGroupLibrary: Option[String] = config("read_group_library")
/** value to put into read-group library (rg-pl) field */
- var read_group_platform: Option[String] = config("read_group_platform")
+ var readGroupPlatform: Option[String] = config("read_group_platform")
def versionRegex = """.* version (.*)""".r
def versionCommand = executable + " --version"
@@ -343,99 +343,99 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
required(executable) +
optional("--dir", dir) +
optional("--db", db) +
- optional("--use-sarray", use_sarray) +
+ optional("--use-sarray", useSarray) +
optional("--kmer", kmer) +
optional("--sampling", sampling) +
optional("--part", part) +
- optional("--input-buffer-size", input_buffer_size) +
- optional("--barcode-length", barcode_length) +
+ optional("--input-buffer-size", inputBufferSize) +
+ optional("--barcode-length", barcodeLength) +
optional("--orientation", orientation) +
- optional("--fastq-id-start", fastq_id_start) +
- optional("--fastq-id-end", fastq_id_end) +
- conditional(force_single_end, "--force-single-end") +
- optional("--filter-chastity", filter_chastity) +
- conditional(allow_pe_name_mismatch, "--allow-pe-name-mismatch") +
+ optional("--fastq-id-start", fastqIdStart) +
+ optional("--fastq-id-end", fastqIdEnd) +
+ conditional(forceSingleEnd, "--force-single-end") +
+ optional("--filter-chastity", filterChastity) +
+ conditional(allowPeNameMismatch, "--allow-pe-name-mismatch") +
conditional(gunzip, "--gunzip") +
conditional(bunzip2, "--bunzip2") +
optional("--batch", batch) +
- optional("--expand-offsets", expand_offsets) +
- optional("--max-mismatches", max_mismatches) +
- optional("--query-unk-mismatch", query_unk_mismatch) +
- optional("--genome-unk-mismatch", genome_unk_mismatch) +
+ optional("--expand-offsets", expandOffsets) +
+ optional("--max-mismatches", maxMismatches) +
+ optional("--query-unk-mismatch", queryUnkMismatch) +
+ optional("--genome-unk-mismatch", genomeUnkMismatch) +
optional("--maxsearch", maxsearch) +
- optional("--terminal-threshold", terminal_threshold) +
- optional("--terminal-output-minlength", terminal_output_minlength) +
- optional("--indel-penalty", indel_penalty) +
- optional("--indel-endlength", indel_endlength) +
- optional("--max-middle-insertions", max_middle_insertions) +
- optional("--max-middle-deletions", max_middle_deletions) +
- optional("--max-end-insertions", max_end_insertions) +
- optional("--max-end-deletions", max_end_deletions) +
- optional("--suboptimal-levels", suboptimal_levels) +
- optional("--adapter-strip", adapter_strip) +
- optional("--trim-mismatch-score", trim_mismatch_score) +
- optional("--trim-indel-score", trim_indel_score) +
+ optional("--terminal-threshold", terminalThreshold) +
+ optional("--terminal-output-minlength", terminalOutputMinlength) +
+ optional("--indel-penalty", indelPenalty) +
+ optional("--indel-endlength", indelEndlength) +
+ optional("--max-middle-insertions", maxMiddleInsertions) +
+ optional("--max-middle-deletions", maxMiddleDeletions) +
+ optional("--max-end-insertions", maxEndInsertions) +
+ optional("--max-end-deletions", maxEndDeletions) +
+ optional("--suboptimal-levels", suboptimalLevels) +
+ optional("--adapter-strip", adapterStrip) +
+ optional("--trim-mismatch-score", trimMismatchScore) +
+ optional("--trim-indel-score", trimIndelScore) +
optional("--snpsdir", snpsdir) +
- optional("--use-snps", use_snps) +
+ optional("--use-snps", useSnps) +
optional("--cmetdir", cmetdir) +
optional("--atoidir", atoidir) +
optional("--mode", mode) +
optional("--tallydir", tallydir) +
- optional("--use-tally", use_tally) +
- optional("--runlengthdir", runlengthdir) +
- optional("--use-runlength", use_runlength) +
+ optional("--use-tally", useTally) +
+ optional("--runlengthdir", runLengthDir) +
+ optional("--use-runlength", useRunlength) +
optional("--nthreads", threads) +
- optional("--gmap-mode", gmap_mode) +
- optional("--trigger-score-for-gmap", trigger_score_for_gmap) +
- optional("--gmap-min-match-length", gmap_min_match_length) +
- optional("--gmap-allowance", gmap_allowance) +
- optional("--max-gmap-pairsearch", max_gmap_pairsearch) +
- optional("--max-gmap-terminal", max_gmap_terminal) +
- optional("--max-gmap-improvement", max_gmap_improvement) +
- optional("--microexon-spliceprob", microexon_spliceprob) +
- optional("--novelsplicing", novelsplicing) +
- optional("--splicingdir", splicingdir) +
- optional("--use-splicing", use_splicing) +
- conditional(ambig_splice_noclip, "--ambig-splice-noclip") +
- optional("--localsplicedist", localsplicedist) +
- optional("--novelend-splicedist", novelend_splicedist) +
- optional("--local-splice-penalty", local_splice_penalty) +
- optional("--distant-splice-penalty", distant_splice_penalty) +
- optional("--distant-splice-endlength", distant_splice_endlength) +
- optional("--shortend-splice-endlength", shortend_splice_endlength) +
- optional("--distant-splice-identity", distant_splice_identity) +
- optional("--antistranded-penalty", antistranded_penalty) +
- conditional(merge_distant_samechr, "--merge-distant-samechr") +
- optional("--pairmax-dna", pairmax_dna) +
- optional("--pairmax-rna", pairmax_rna) +
- optional("--pairexpect", pairexpect) +
- optional("--pairdev", pairdev) +
- optional("--quality-protocol", quality_protocol) +
- optional("--quality-zero-score", quality_zero_score) +
- optional("--quality-print-shift", quality_print_shift) +
+ optional("--gmap-mode", gmapMode) +
+ optional("--trigger-score-for-gmap", triggerScoreForGmap) +
+ optional("--gmap-min-match-length", gmapMinMatchLength) +
+ optional("--gmap-allowance", gmapAllowance) +
+ optional("--max-gmap-pairsearch", maxGmapPairsearch) +
+ optional("--max-gmap-terminal", maxGmapTerminal) +
+ optional("--max-gmap-improvement", maxGmapImprovement) +
+ optional("--microexon-spliceprob", microExonSpliceprob) +
+ optional("--novelsplicing", novelSplicing) +
+ optional("--splicingdir", splicingDir) +
+ optional("--use-splicing", useSplicing) +
+ conditional(ambigSpliceNoclip, "--ambig-splice-noclip") +
+ optional("--localsplicedist", localSpliceDist) +
+ optional("--novelend-splicedist", novelEndSplicedist) +
+ optional("--local-splice-penalty", localSplicePenalty) +
+ optional("--distant-splice-penalty", distantSplicePenalty) +
+ optional("--distant-splice-endlength", distantSpliceEndlength) +
+ optional("--shortend-splice-endlength", shortendSpliceEndlength) +
+ optional("--distant-splice-identity", distantSpliceIdentity) +
+ optional("--antistranded-penalty", antiStrandedPenalty) +
+ conditional(mergeDistantSamechr, "--merge-distant-samechr") +
+ optional("--pairmax-dna", pairmaxDna) +
+ optional("--pairmax-rna", pairmaxRna) +
+ optional("--pairexpect", pairExpect) +
+ optional("--pairdev", pairDev) +
+ optional("--quality-protocol", qualityProtocol) +
+ optional("--quality-zero-score", qualityZeroScore) +
+ optional("--quality-print-shift", qualityPrintShift) +
optional("--npaths", npaths) +
- conditional(quiet_if_excessive, "--quiet-if-excessive") +
+ conditional(quietIfExcessive, "--quiet-if-excessive") +
conditional(ordered, "--ordered") +
- conditional(show_refdiff, "--show-refdiff") +
- conditional(clip_overlap, "--clip-overlap") +
- conditional(print_snps, "--print-snps") +
- conditional(failsonly, "--failsonly") +
- conditional(nofails, "--nofails") +
- conditional(fails_as_input, "--fails-as-input") +
+ conditional(showRefdiff, "--show-refdiff") +
+ conditional(clipOverlap, "--clip-overlap") +
+ conditional(printSnps, "--print-snps") +
+ conditional(failsOnly, "--failsonly") +
+ conditional(noFails, "--nofails") +
+ conditional(failsAsInput, "--fails-as-input") +
optional("--format", format) +
- optional("--split-output", split_output) +
- conditional(append_output, "--append-output") +
- optional("--output-buffer-size", output_buffer_size) +
- conditional(no_sam_headers, "--no-sam-headers") +
- optional("--sam-headers-batch", sam_headers_batch) +
- conditional(sam_use_0M, "--sam-use-0M") +
- conditional(sam_multiple_primaries, "--sam-multiple-primaries") +
- conditional(force_xs_dir, "--force-xs-dir") +
- conditional(md_lowercase_snp, "--md-lowercase-snp") +
- optional("--read-group-id", read_group_id) +
- optional("--read-group-name", read_group_name) +
- optional("--read-group-library", read_group_library) +
- optional("--read-group-platform", read_group_platform) +
+ optional("--split-output", splitOutput) +
+ conditional(appendOutput, "--append-output") +
+ optional("--output-buffer-size", outputBufferSize) +
+ conditional(noSamHeaders, "--no-sam-headers") +
+ optional("--sam-headers-batch", samHeadersBatch) +
+ conditional(samUse0M, "--sam-use-0M") +
+ conditional(samMultiplePrimaries, "--sam-multiple-primaries") +
+ conditional(forceXsDir, "--force-xs-dir") +
+ conditional(mdLowercaseSnp, "--md-lowercase-snp") +
+ optional("--read-group-id", readGroupId) +
+ optional("--read-group-name", readGroupName) +
+ optional("--read-group-library", readGroupLibrary) +
+ optional("--read-group-platform", readGroupPlatform) +
repeat(input) +
" > " + required(output)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
index e4470ffec..f8623c82f 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
@@ -29,10 +29,10 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Vers
var input: List[File] = _
@Output(doc = "Unidentified reads", required = false)
- var unclassified_out: Option[File] = None
+ var unclassifiedOut: Option[File] = None
@Output(doc = "Identified reads", required = false)
- var classified_out: Option[File] = None
+ var classifiedOut: Option[File] = None
@Output(doc = "Output with hits per sequence")
var output: File = _
@@ -69,8 +69,8 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Vers
optional("--threads", nCoresRequest) +
conditional(quick, "--quick") +
optional("--min_hits", minHits) +
- optional("--unclassified-out ", unclassified_out) +
- optional("--classified-out ", classified_out) +
+ optional("--unclassified-out ", unclassifiedOut) +
+ optional("--classified-out ", classifiedOut) +
required("--output", output) +
conditional(preLoad, "--preload") +
conditional(paired, "--paired") +
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
index aa6e825bb..00b29970d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
@@ -39,7 +39,7 @@ class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction wit
}
var db: File = config("db")
- var show_zeros: Boolean = config("show_zeros", default = false)
+ var showZeros: Boolean = config("show_zeros", default = false)
@Input(doc = "Input raw kraken analysis")
var input: File = _
@@ -49,7 +49,7 @@ class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction wit
def cmdLine: String = required(executable) +
required("--db", db) +
- conditional(show_zeros, "--show-zeros") +
+ conditional(showZeros, "--show-zeros") +
required(input) +
" > " + required(output)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index 10fb47713..76a0c4ae5 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -29,22 +29,22 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var control: File = _
@Output(doc = "Output file NARROWPEAKS")
- private var output_narrow: File = _
+ private var outputNarrow: File = _
@Output(doc = "Output file BROADPEAKS")
- private var output_broad: File = _
+ private var outputBroad: File = _
@Output(doc = "Output in Excel format")
- private var output_xls: File = _
+ private var outputXls: File = _
@Output(doc = "R script with Bimodal model")
- private var output_r: File = _
+ private var outputR: File = _
@Output(doc = "Output file Bedgraph")
- private var output_bdg: File = _
+ private var outputBdg: File = _
@Output(doc = "Output file gappedPeak")
- private var output_gapped: File = _
+ private var outputGapped: File = _
var fileformat: Option[String] = config("fileformat")
var gsize: Option[Float] = config("gsize")
@@ -77,12 +77,12 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
override def beforeGraph(): Unit = {
if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
- output_narrow = new File(outputdir + name.get + ".narrowPeak")
- output_broad = new File(outputdir + name.get + ".broadPeak")
- output_xls = new File(outputdir + name.get + ".xls")
- output_bdg = new File(outputdir + name.get + ".bdg")
- output_r = new File(outputdir + name.get + ".r")
- output_gapped = new File(outputdir + name.get + ".gappedPeak")
+ outputNarrow = new File(outputdir + name.get + ".narrowPeak")
+ outputBroad = new File(outputdir + name.get + ".broadPeak")
+ outputXls = new File(outputdir + name.get + ".xls")
+ outputBdg = new File(outputdir + name.get + ".bdg")
+ outputR = new File(outputdir + name.get + ".r")
+ outputGapped = new File(outputdir + name.get + ".gappedPeak")
}
/** Returns command to execute */
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index 5769a9763..a3b3fc84b 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -116,12 +116,12 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var ploidy: Option[File] = config("ploidy")
var detectDD: Boolean = config("detect_DD", default = false)
- var MAX_DD_BREAKPOINT_DISTANCE: Option[Int] = config("MAX_DD_BREAKPOINT_DISTANCE")
- var MAX_DISTANCE_CLUSTER_READS: Option[Int] = config("MAX_DISTANCE_CLUSTER_READS")
- var MIN_DD_CLUSTER_SIZE: Option[Int] = config("MIN_DD_CLUSTER_SIZE")
- var MIN_DD_BREAKPOINT_SUPPORT: Option[Int] = config("MIN_DD_BREAKPOINT_SUPPORT")
- var MIN_DD_MAP_DISTANCE: Option[Int] = config("MIN_DD_MAP_DISTANCE")
- var DD_REPORT_DUPLICATION_READS: Option[Int] = config("DD_REPORT_DUPLICATION_READS")
+ var maxDdBreakpointDistance: Option[Int] = config("max_dd_breakpoint_distance")
+ var maxDistanceClusterReads: Option[Int] = config("max_distance_cluster_reads")
+ var minDdClusterSize: Option[Int] = config("min_dd_cluster_size")
+ var minDdBreakpointSupport: Option[Int] = config("min_dd_Breakpoint_support")
+ var minDdMapDistance: Option[Int] = config("min_dd_map_distance")
+ var ddReportDuplicationReads: Option[Int] = config("dd_report_duplication_reads")
override def beforeGraph: Unit = {
if (reference == null) reference = referenceFasta()
@@ -201,12 +201,12 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
optional("--name_of_logfile", nameOfLogfile) +
optional("--Ploidy", ploidy) +
conditional(detectDD, "detect_DD") +
- optional("--MAX_DD_BREAKPOINT_DISTANCE", MAX_DD_BREAKPOINT_DISTANCE) +
- optional("--MAX_DISTANCE_CLUSTER_READS", MAX_DISTANCE_CLUSTER_READS) +
- optional("--MIN_DD_CLUSTER_SIZE", MIN_DD_CLUSTER_SIZE) +
- optional("--MIN_DD_BREAKPOINT_SUPPORT", MIN_DD_BREAKPOINT_SUPPORT) +
- optional("--MIN_DD_MAP_DISTANCE", MIN_DD_MAP_DISTANCE) +
- optional("--DD_REPORT_DUPLICATION_READS", DD_REPORT_DUPLICATION_READS)
+ optional("--MAX_DD_BREAKPOINT_DISTANCE", maxDdBreakpointDistance) +
+ optional("--MAX_DISTANCE_CLUSTER_READS", maxDistanceClusterReads) +
+ optional("--MIN_DD_CLUSTER_SIZE", minDdClusterSize) +
+ optional("--MIN_DD_BREAKPOINT_SUPPORT", minDdBreakpointSupport) +
+ optional("--MIN_DD_MAP_DISTANCE", minDdMapDistance) +
+ optional("--DD_REPORT_DUPLICATION_READS", ddReportDuplicationReads)
}
object PindelCaller {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
index b41dbfd0d..8ed230df3 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala
@@ -16,38 +16,38 @@ class AssignTaxonomy(val root: Configurable) extends BiopetCommandLineFunction w
var inputFasta: File = _
@Input(required = false)
- var read_1_seqs_fp: Option[File] = None
+ var read1SeqsFp: Option[File] = None
@Input(required = false)
- var read_2_seqs_fp: Option[File] = None
+ var read2SeqsFp: Option[File] = None
@Input(required = false)
- var id_to_taxonomy_fp: Option[File] = config("id_to_taxonomy_fp")
+ var idToTaxonomyFp: Option[File] = config("id_to_taxonomy_fp")
@Input(required = false)
- var reference_seqs_fp: Option[File] = config("reference_seqs_fp")
+ var referenceSeqsFp: Option[File] = config("reference_seqs_fp")
@Input(required = false)
- var training_data_properties_fp: Option[File] = config("training_data_properties_fp")
+ var trainingDataPropertiesFp: Option[File] = config("training_data_properties_fp")
- var single_ok: Boolean = config("single_ok", default = false)
- var no_single_ok_generic: Boolean = config("no_single_ok_generic", default = false)
+ var singleOk: Boolean = config("single_ok", default = false)
+ var noSingleOkGeneric: Boolean = config("no_single_ok_generic", default = false)
- var amplicon_id_regex: Option[String] = config("amplicon_id_regex")
- var header_id_regex: Option[String] = config("header_id_regex")
- var assignment_method: Option[String] = config("assignment_method")
- var sortmerna_db: Option[String] = config("sortmerna_db")
- var sortmerna_e_value: Option[String] = config("sortmerna_e_value")
- var sortmerna_coverage: Option[String] = config("sortmerna_coverage")
- var sortmerna_best_N_alignments: Option[String] = config("sortmerna_best_N_alignments")
- var sortmerna_threads: Option[String] = config("sortmerna_threads")
- var blast_db: Option[String] = config("blast_db")
+ var ampliconIdRegex: Option[String] = config("amplicon_id_regex")
+ var headerIdRegex: Option[String] = config("header_id_regex")
+ var assignmentMethod: Option[String] = config("assignment_method")
+ var sortmernaDb: Option[String] = config("sortmerna_db")
+ var sortmernaEValue: Option[String] = config("sortmerna_e_value")
+ var sortmernaCoverage: Option[String] = config("sortmerna_coverage")
+ var sortmernaBestNAlignments: Option[String] = config("sortmerna_best_N_alignments")
+ var sortmernaThreads: Option[String] = config("sortmerna_threads")
+ var blastDb: Option[String] = config("blast_db")
var confidence: Option[String] = config("confidence")
- var min_consensus_fraction: Option[String] = config("min_consensus_fraction")
+ var minConsensusFraction: Option[String] = config("min_consensus_fraction")
var similarity: Option[String] = config("similarity")
- var uclust_max_accepts: Option[String] = config("uclust_max_accepts")
- var rdp_max_memory: Option[String] = config("rdp_max_memory")
- var blast_e_value: Option[String] = config("blast_e_value")
+ var uclustMaxAccepts: Option[String] = config("uclust_max_accepts")
+ var rdpMaxMemory: Option[String] = config("rdp_max_memory")
+ var blastEValue: Option[String] = config("blast_e_value")
var outputDir: File = _
def versionCommand = executable + " --version"
@@ -61,27 +61,27 @@ class AssignTaxonomy(val root: Configurable) extends BiopetCommandLineFunction w
def cmdLine = executable +
required("-i", inputFasta) +
- optional("--read_1_seqs_fp", read_1_seqs_fp) +
- optional("--read_2_seqs_fp", read_2_seqs_fp) +
- optional("-t", id_to_taxonomy_fp) +
- optional("-r", reference_seqs_fp) +
- optional("-p", training_data_properties_fp) +
- optional("--amplicon_id_regex", amplicon_id_regex) +
- optional("--header_id_regex", header_id_regex) +
- optional("--assignment_method", assignment_method) +
- optional("--sortmerna_db", sortmerna_db) +
- optional("--sortmerna_e_value", sortmerna_e_value) +
- optional("--sortmerna_coverage", sortmerna_coverage) +
- optional("--sortmerna_best_N_alignments", sortmerna_best_N_alignments) +
- optional("--sortmerna_threads", sortmerna_threads) +
- optional("--blast_db", blast_db) +
+ optional("--read_1_seqs_fp", read1SeqsFp) +
+ optional("--read_2_seqs_fp", read2SeqsFp) +
+ optional("-t", idToTaxonomyFp) +
+ optional("-r", referenceSeqsFp) +
+ optional("-p", trainingDataPropertiesFp) +
+ optional("--amplicon_id_regex", ampliconIdRegex) +
+ optional("--header_id_regex", headerIdRegex) +
+ optional("--assignment_method", assignmentMethod) +
+ optional("--sortmerna_db", sortmernaDb) +
+ optional("--sortmerna_e_value", sortmernaEValue) +
+ optional("--sortmerna_coverage", sortmernaCoverage) +
+ optional("--sortmerna_best_N_alignments", sortmernaBestNAlignments) +
+ optional("--sortmerna_threads", sortmernaThreads) +
+ optional("--blast_db", blastDb) +
optional("--confidence", confidence) +
- optional("--min_consensus_fraction", min_consensus_fraction) +
+ optional("--min_consensus_fraction", minConsensusFraction) +
optional("--similarity", similarity) +
- optional("--uclust_max_accepts", uclust_max_accepts) +
- optional("--rdp_max_memory", rdp_max_memory) +
- optional("--blast_e_value", blast_e_value) +
+ optional("--uclust_max_accepts", uclustMaxAccepts) +
+ optional("--rdp_max_memory", rdpMaxMemory) +
+ optional("--blast_e_value", blastEValue) +
required("--output_dir", outputDir) +
- conditional(single_ok, "--single_ok") +
- conditional(no_single_ok_generic, "--no_single_ok_generic")
+ conditional(singleOk, "--single_ok") +
+ conditional(noSingleOkGeneric, "--no_single_ok_generic")
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
index a538e97a1..1a3d61b30 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/MergeOtuMaps.scala
@@ -21,7 +21,7 @@ class MergeOtuMaps(val root: Configurable) extends BiopetCommandLineFunction wit
@Output(required = true)
var outputFile: File = _
- var failures_fp: Option[File] = None
+ var failuresFp: Option[File] = None
override def beforeGraph(): Unit = {
super.beforeGraph()
@@ -35,5 +35,5 @@ class MergeOtuMaps(val root: Configurable) extends BiopetCommandLineFunction wit
case _ => ""
}) +
required("-o", outputFile) +
- optional("--failures_fp", failures_fp)
+ optional("--failures_fp", failuresFp)
}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
index 265a6d21f..d0ddad3af 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
@@ -23,18 +23,18 @@ class PickClosedReferenceOtus(val root: Configurable) extends BiopetCommandLineF
def versionRegex = """Version: (.*)""".r
@Input(required = false)
- var parameter_fp: Option[File] = config("parameter_fp")
+ var parameterFp: Option[File] = config("parameter_fp")
@Input(required = false)
- var reference_fp: Option[File] = config("reference_fp")
+ var referenceFp: Option[File] = config("reference_fp")
@Input(required = false)
- var taxonomy_fp: Option[File] = config("taxonomy_fp")
+ var taxonomyFp: Option[File] = config("taxonomy_fp")
- var assign_taxonomy: Boolean = config("assign_taxonomy", default = false)
+ var assignTaxonomy: Boolean = config("assign_taxonomy", default = false)
var force: Boolean = config("force", default = false)
- var print_only: Boolean = config("print_only", default = false)
- var suppress_taxonomy_assignment: Boolean = config("suppress_taxonomy_assignment", default = false)
+ var printOnly: Boolean = config("print_only", default = false)
+ var suppressTaxonomyAssignment: Boolean = config("suppress_taxonomy_assignment", default = false)
def otuTable = new File(outputDir, "otu_table.biom")
def otuMap = new File(outputDir, "uclust_ref_picked_otus" + File.separator + "seqs_otus.txt")
@@ -49,13 +49,13 @@ class PickClosedReferenceOtus(val root: Configurable) extends BiopetCommandLineF
def cmdLine = executable + required("-f") +
required("-i", inputFasta) +
required("-o", outputDir) +
- optional("--reference_fp", reference_fp) +
- optional("--parameter_fp", parameter_fp) +
- optional("--taxonomy_fp", taxonomy_fp) +
- conditional(assign_taxonomy, "--assign_taxonomy") +
+ optional("--reference_fp", referenceFp) +
+ optional("--parameter_fp", parameterFp) +
+ optional("--taxonomy_fp", taxonomyFp) +
+ conditional(assignTaxonomy, "--assign_taxonomy") +
conditional(force, "--force") +
- conditional(print_only, "--print_only") +
- conditional(suppress_taxonomy_assignment, "--suppress_taxonomy_assignment") +
+ conditional(printOnly, "--print_only") +
+ conditional(suppressTaxonomyAssignment, "--suppress_taxonomy_assignment") +
(if (threads > 1) required("-a") + required("-O", threads) else "")
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
index f83c59aa9..47c7fde0a 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickOtus.scala
@@ -22,59 +22,59 @@ class PickOtus(val root: Configurable) extends BiopetCommandLineFunction with Ve
def versionCommand = executable + " --version"
def versionRegex = """Version: (.*)""".r
- var otu_picking_method: Option[String] = config("otu_picking_method")
- var clustering_algorithm: Option[String] = config("clustering_algorithm")
- var max_cdhit_memory: Option[Int] = config("max_cdhit_memory")
- var refseqs_fp: Option[String] = config("refseqs_fp")
- var blast_db: Option[String] = config("blast_db")
- var max_e_value_blast: Option[String] = config("max_e_value_blast")
- var sortmerna_db: Option[String] = config("sortmerna_db")
- var sortmerna_e_value: Option[Double] = config("sortmerna_e_value")
- var sortmerna_coverage: Option[Double] = config("sortmerna_coverage")
- var sortmerna_tabular: Boolean = config("sortmerna_tabular", default = false)
- var sortmerna_best_N_alignments: Option[Int] = config("sortmerna_best_N_alignments")
- var sortmerna_max_pos: Option[Int] = config("sortmerna_max_pos")
- var min_aligned_percent: Option[Double] = config("min_aligned_percent")
+ var otuPickingMethod: Option[String] = config("otu_picking_method")
+ var clusteringAlgorithm: Option[String] = config("clustering_algorithm")
+ var maxCdhitMemory: Option[Int] = config("max_cdhit_memory")
+ var refseqsFp: Option[String] = config("refseqs_fp")
+ var blastDb: Option[String] = config("blast_db")
+ var maxEValueBlast: Option[String] = config("max_e_value_blast")
+ var sortmernaDb: Option[String] = config("sortmerna_db")
+ var sortmernaEValue: Option[Double] = config("sortmerna_e_value")
+ var sortmernaCoverage: Option[Double] = config("sortmerna_coverage")
+ var sortmernaTabular: Boolean = config("sortmerna_tabular", default = false)
+ var sortmernaBestNAlignments: Option[Int] = config("sortmerna_best_N_alignments")
+ var sortmernaMaxPos: Option[Int] = config("sortmerna_max_pos")
+ var minAlignedPercent: Option[Double] = config("min_aligned_percent")
var similarity: Option[Double] = config("similarity")
- var sumaclust_exact: Option[String] = config("sumaclust_exact")
- var sumaclust_l: Boolean = config("sumaclust_l", default = false)
- var denovo_otu_id_prefix: Option[String] = config("denovo_otu_id_prefix")
- var swarm_resolution: Option[String] = config("swarm_resolution")
- var trie_reverse_seqs: Boolean = config("trie_reverse_seqs", default = false)
- var prefix_prefilter_length: Option[String] = config("prefix_prefilter_length")
- var trie_prefilter: Option[String] = config("trie_prefilter")
- var prefix_length: Option[String] = config("prefix_length")
- var suffix_length: Option[String] = config("suffix_length")
- var enable_rev_strand_match: Boolean = config("enable_rev_strand_match", default = false)
- var suppress_presort_by_abundance_uclust: Boolean = config("suppress_presort_by_abundance_uclust", default = false)
- var optimal_uclust: Boolean = config("optimal_uclust", default = false)
- var exact_uclust: Boolean = config("exact_uclust", default = false)
- var user_sort: Boolean = config("user_sort", default = false)
- var suppress_new_clusters: Boolean = config("suppress_new_clusters", default = false)
- var max_accepts: Option[String] = config("max_accepts")
- var max_rejects: Option[String] = config("max_rejects")
+ var sumaclustExact: Option[String] = config("sumaclust_exact")
+ var sumaclustL: Boolean = config("sumaclust_l", default = false)
+ var denovoOtuIdPrefix: Option[String] = config("denovo_otu_id_prefix")
+ var swarmResolution: Option[String] = config("swarm_resolution")
+ var trieReverseSeqs: Boolean = config("trie_reverse_seqs", default = false)
+ var prefixPrefilterLength: Option[String] = config("prefix_prefilter_length")
+ var triePrefilter: Option[String] = config("trie_prefilter")
+ var prefixLength: Option[String] = config("prefix_length")
+ var suffixLength: Option[String] = config("suffix_length")
+ var enableRevStrandMatch: Boolean = config("enable_rev_strand_match", default = false)
+ var suppressPresortByAbundanceUclust: Boolean = config("suppress_presort_by_abundance_uclust", default = false)
+ var optimalUclust: Boolean = config("optimal_uclust", default = false)
+ var exactUclust: Boolean = config("exact_uclust", default = false)
+ var userSort: Boolean = config("user_sort", default = false)
+ var suppressNewClusters: Boolean = config("suppress_new_clusters", default = false)
+ var maxAccepts: Option[String] = config("max_accepts")
+ var maxRejects: Option[String] = config("max_rejects")
var stepwords: Option[String] = config("stepwords")
- var word_length: Option[String] = config("word_length")
- var suppress_uclust_stable_sort: Boolean = config("suppress_uclust_stable_sort", default = false)
- var suppress_prefilter_exact_match: Boolean = config("suppress_prefilter_exact_match", default = false)
- var save_uc_files: Boolean = config("save_uc_files", default = false)
- var percent_id_err: Option[String] = config("percent_id_err")
- var minsize: Option[String] = config("minsize")
- var abundance_skew: Option[String] = config("abundance_skew")
- var db_filepath: Option[String] = config("db_filepath")
- var perc_id_blast: Option[String] = config("perc_id_blast")
- var de_novo_chimera_detection: Boolean = config("de_novo_chimera_detection", default = false)
- var suppress_de_novo_chimera_detection: Boolean = config("suppress_de_novo_chimera_detection", default = false)
- var reference_chimera_detection: Option[String] = config("reference_chimera_detection")
- var suppress_reference_chimera_detection: Option[String] = config("suppress_reference_chimera_detection")
- var cluster_size_filtering: Option[String] = config("cluster_size_filtering")
- var suppress_cluster_size_filtering: Option[String] = config("suppress_cluster_size_filtering")
- var remove_usearch_logs: Boolean = config("remove_usearch_logs", default = false)
- var derep_fullseq: Boolean = config("derep_fullseq", default = false)
- var non_chimeras_retention: Option[String] = config("non_chimeras_retention")
+ var wordLength: Option[String] = config("word_length")
+ var suppressUclustStableSort: Boolean = config("suppress_uclust_stable_sort", default = false)
+ var suppressPrefilterExactMatch: Boolean = config("suppress_prefilter_exact_match", default = false)
+ var saveUcFiles: Boolean = config("save_uc_files", default = false)
+ var percentIdErr: Option[String] = config("percent_id_err")
+ var minSize: Option[String] = config("minsize")
+ var abundanceSkew: Option[String] = config("abundance_skew")
+ var dbFilepath: Option[String] = config("db_filepath")
+ var percIdBlast: Option[String] = config("perc_id_blast")
+ var deNovoChimeraDetection: Boolean = config("de_novo_chimera_detection", default = false)
+ var suppressDeNovoChimeraDetection: Boolean = config("suppress_de_novo_chimera_detection", default = false)
+ var referenceChimeraDetection: Option[String] = config("reference_chimera_detection")
+ var suppressReferenceChimeraDetection: Option[String] = config("suppress_reference_chimera_detection")
+ var clusterSizeFiltering: Option[String] = config("cluster_size_filtering")
+ var suppressClusterSizeFiltering: Option[String] = config("suppress_cluster_size_filtering")
+ var removeUsearchLogs: Boolean = config("remove_usearch_logs", default = false)
+ var derepFullseq: Boolean = config("derep_fullseq", default = false)
+ var nonChimerasRetention: Option[String] = config("non_chimeras_retention")
var minlen: Option[String] = config("minlen")
- var usearch_fast_cluster: Boolean = config("usearch_fast_cluster", default = false)
- var usearch61_sort_method: Option[String] = config("usearch61_sort_method")
+ var usearchFastCluster: Boolean = config("usearch_fast_cluster", default = false)
+ var usearch61SortMethod: Option[String] = config("usearch61_sort_method")
var sizeorder: Boolean = config("sizeorder", default = false)
private lazy val name = inputFasta.getName.stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna")
@@ -93,59 +93,59 @@ class PickOtus(val root: Configurable) extends BiopetCommandLineFunction with Ve
def cmdLine = executable +
required("-i", inputFasta) +
required("-o", outputDir) +
- optional("-m", otu_picking_method) +
- optional("-c", clustering_algorithm) +
- optional("-M", max_cdhit_memory) +
- optional("-r", refseqs_fp) +
- optional("-b", blast_db) +
- optional("-e", max_e_value_blast) +
- optional("--sortmerna_db", sortmerna_db) +
- optional("--sortmerna_e_value", sortmerna_e_value) +
- optional("--sortmerna_coverage", sortmerna_coverage) +
- conditional(sortmerna_tabular, "--sortmerna_tabular") +
- optional("--sortmerna_best_N_alignments", sortmerna_best_N_alignments) +
- optional("--sortmerna_max_pos", sortmerna_max_pos) +
- optional("--min_aligned_percent", min_aligned_percent) +
+ optional("-m", otuPickingMethod) +
+ optional("-c", clusteringAlgorithm) +
+ optional("-M", maxCdhitMemory) +
+ optional("-r", refseqsFp) +
+ optional("-b", blastDb) +
+ optional("-e", maxEValueBlast) +
+ optional("--sortmerna_db", sortmernaDb) +
+ optional("--sortmerna_e_value", sortmernaEValue) +
+ optional("--sortmerna_coverage", sortmernaCoverage) +
+ conditional(sortmernaTabular, "--sortmerna_tabular") +
+ optional("--sortmerna_best_N_alignments", sortmernaBestNAlignments) +
+ optional("--sortmerna_max_pos", sortmernaMaxPos) +
+ optional("--min_aligned_percent", minAlignedPercent) +
optional("--similarity", similarity) +
- optional("--sumaclust_exact", sumaclust_exact) +
- conditional(sumaclust_l, "--sumaclust_l") +
- optional("--denovo_otu_id_prefix", denovo_otu_id_prefix) +
- optional("--swarm_resolution", swarm_resolution) +
- conditional(trie_reverse_seqs, "--trie_reverse_seqs") +
- optional("--prefix_prefilter_length", prefix_prefilter_length) +
- optional("--trie_prefilter", trie_prefilter) +
- optional("--prefix_length", prefix_length) +
- optional("--suffix_length", suffix_length) +
- conditional(enable_rev_strand_match, "--enable_rev_strand_match") +
- conditional(suppress_presort_by_abundance_uclust, "--suppress_presort_by_abundance_uclust") +
- conditional(optimal_uclust, "--optimal_uclust") +
- conditional(exact_uclust, "--exact_uclust") +
- conditional(user_sort, "--user_sort") +
- conditional(suppress_new_clusters, "--suppress_new_clusters") +
- optional("--max_accepts", max_accepts) +
- optional("--max_rejects", max_rejects) +
+ optional("--sumaclust_exact", sumaclustExact) +
+ conditional(sumaclustL, "--sumaclust_l") +
+ optional("--denovo_otu_id_prefix", denovoOtuIdPrefix) +
+ optional("--swarm_resolution", swarmResolution) +
+ conditional(trieReverseSeqs, "--trie_reverse_seqs") +
+ optional("--prefix_prefilter_length", prefixPrefilterLength) +
+ optional("--trie_prefilter", triePrefilter) +
+ optional("--prefix_length", prefixLength) +
+ optional("--suffix_length", suffixLength) +
+ conditional(enableRevStrandMatch, "--enable_rev_strand_match") +
+ conditional(suppressPresortByAbundanceUclust, "--suppress_presort_by_abundance_uclust") +
+ conditional(optimalUclust, "--optimal_uclust") +
+ conditional(exactUclust, "--exact_uclust") +
+ conditional(userSort, "--user_sort") +
+ conditional(suppressNewClusters, "--suppress_new_clusters") +
+ optional("--max_accepts", maxAccepts) +
+ optional("--max_rejects", maxRejects) +
optional("--stepwords", stepwords) +
- optional("--word_length", word_length) +
- conditional(suppress_uclust_stable_sort, "--suppress_uclust_stable_sort") +
- conditional(suppress_prefilter_exact_match, "--suppress_prefilter_exact_match") +
- conditional(save_uc_files, "--save_uc_files") +
- optional("--percent_id_err", percent_id_err) +
- optional("--minsize", minsize) +
- optional("--abundance_skew", abundance_skew) +
- optional("--db_filepath", db_filepath) +
- optional("--perc_id_blast", perc_id_blast) +
- conditional(de_novo_chimera_detection, "--de_novo_chimera_detection") +
- conditional(suppress_de_novo_chimera_detection, "--suppress_de_novo_chimera_detection") +
- optional("--reference_chimera_detection", reference_chimera_detection) +
- optional("--suppress_reference_chimera_detection", suppress_reference_chimera_detection) +
- optional("--cluster_size_filtering", cluster_size_filtering) +
- optional("--suppress_cluster_size_filtering", suppress_cluster_size_filtering) +
- conditional(remove_usearch_logs, "--remove_usearch_logs") +
- conditional(derep_fullseq, "--derep_fullseq") +
- optional("--non_chimeras_retention", non_chimeras_retention) +
+ optional("--word_length", wordLength) +
+ conditional(suppressUclustStableSort, "--suppress_uclust_stable_sort") +
+ conditional(suppressPrefilterExactMatch, "--suppress_prefilter_exact_match") +
+ conditional(saveUcFiles, "--save_uc_files") +
+ optional("--percent_id_err", percentIdErr) +
+ optional("--minsize", minSize) +
+ optional("--abundance_skew", abundanceSkew) +
+ optional("--db_filepath", dbFilepath) +
+ optional("--perc_id_blast", percIdBlast) +
+ conditional(deNovoChimeraDetection, "--de_novo_chimera_detection") +
+ conditional(suppressDeNovoChimeraDetection, "--suppress_de_novo_chimera_detection") +
+ optional("--reference_chimera_detection", referenceChimeraDetection) +
+ optional("--suppress_reference_chimera_detection", suppressReferenceChimeraDetection) +
+ optional("--cluster_size_filtering", clusterSizeFiltering) +
+ optional("--suppress_cluster_size_filtering", suppressClusterSizeFiltering) +
+ conditional(removeUsearchLogs, "--remove_usearch_logs") +
+ conditional(derepFullseq, "--derep_fullseq") +
+ optional("--non_chimeras_retention", nonChimerasRetention) +
optional("--minlen", minlen) +
- conditional(usearch_fast_cluster, "--usearch_fast_cluster") +
- optional("--usearch61_sort_method", usearch61_sort_method) +
+ conditional(usearchFastCluster, "--usearch_fast_cluster") +
+ optional("--usearch61_sort_method", usearch61SortMethod) +
conditional(sizeorder, "--sizeorder") +
optional("--threads", threads)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
index 5496c673c..a29f82109 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala
@@ -22,7 +22,7 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
var logFile: Option[File] = None
@Input(required = false)
- var reference_seqs_fp: Option[File] = config("reference_seqs_fp")
+ var referenceSeqsFp: Option[File] = config("reference_seqs_fp")
@Input(required = false)
var fastaInput: Option[File] = None
@@ -32,14 +32,14 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
def versionCommand = executable + " --version"
def versionRegex = """Version: (.*)""".r
- var rep_set_picking_method: Option[String] = config("rep_set_picking_method")
+ var repSetPickingMethod: Option[String] = config("rep_set_picking_method")
def cmdLine = executable +
required("-i", inputFile) +
required("-o", outputFasta) +
- optional("-m", rep_set_picking_method) +
+ optional("-m", repSetPickingMethod) +
optional("-f", fastaInput) +
optional("-l", logFile) +
optional("-s", sortBy) +
- optional("-r", reference_seqs_fp)
+ optional("-r", referenceSeqsFp)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
index 25db2dd9a..6b02239a7 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
@@ -22,22 +22,22 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
var v: Option[String] = config("v")
var m: Option[String] = config("m")
var b: Option[String] = config("b")
- var store_qual_scores: Boolean = config("store_qual_scores", default = false)
- var sample_ids: List[String] = Nil
- var store_demultiplexed_fastq: Boolean = config("store_demultiplexed_fastq", default = false)
- var retain_unassigned_reads: Boolean = config("retain_unassigned_reads", default = false)
+ var storeQualScores: Boolean = config("store_qual_scores", default = false)
+ var sampleIds: List[String] = Nil
+ var storeDemultiplexedFastq: Boolean = config("store_demultiplexed_fastq", default = false)
+ var retainUnassignedReads: Boolean = config("retain_unassigned_reads", default = false)
var r: Option[Int] = config("r")
var p: Option[Double] = config("p")
var n: Option[Int] = config("n")
var s: Option[Int] = config("s")
- var rev_comp_barcode: Boolean = config("rev_comp_barcode", default = false)
- var rev_comp_mapping_barcodes: Boolean = config("rev_comp_mapping_barcodes", default = false)
- var rev_comp: Boolean = config("rev_comp", default = false)
+ var revCompBarcode: Boolean = config("rev_comp_barcode", default = false)
+ var revCompMappingBarcodes: Boolean = config("rev_comp_mapping_barcodes", default = false)
+ var revComp: Boolean = config("rev_comp", default = false)
var q: Option[Int] = config("q")
- var last_bad_quality_char: Option[String] = config("last_bad_quality_char")
- var barcode_type: Option[String] = config("barcode_type")
- var max_barcode_errors: Option[Double] = config("max_barcode_errors")
- var phred_offset: Option[String] = config("phred_offset")
+ var lastBadQualityChar: Option[String] = config("last_bad_quality_char")
+ var barcodeType: Option[String] = config("barcode_type")
+ var maxBarcodeErrors: Option[Double] = config("max_barcode_errors")
+ var phredOffset: Option[String] = config("phred_offset")
def outputSeqs = new File(outputDir, "seqs.fna")
@@ -52,25 +52,25 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
optional("-v", v) +
optional("-m", m) +
optional("-b", b) +
- conditional(store_qual_scores, "--store_qual_scores") +
- (sample_ids match {
+ conditional(storeQualScores, "--store_qual_scores") +
+ (sampleIds match {
case l: List[_] if l.nonEmpty => optional("--sample_ids", l.mkString(","))
case _ => ""
}) +
- conditional(store_demultiplexed_fastq, "--store_demultiplexed_fastq") +
- conditional(retain_unassigned_reads, "--retain_unassigned_reads") +
+ conditional(storeDemultiplexedFastq, "--store_demultiplexed_fastq") +
+ conditional(retainUnassignedReads, "--retain_unassigned_reads") +
optional("-r", r) +
optional("-p", p) +
optional("-n", n) +
optional("-s", s) +
- conditional(rev_comp_barcode, "--rev_comp_barcode") +
- conditional(rev_comp_mapping_barcodes, "--rev_comp_mapping_barcodes") +
- conditional(rev_comp, "--rev_comp") +
+ conditional(revCompBarcode, "--rev_comp_barcode") +
+ conditional(revCompMappingBarcodes, "--rev_comp_mapping_barcodes") +
+ conditional(revComp, "--rev_comp") +
optional("-q", q) +
- optional("--last_bad_quality_char", last_bad_quality_char) +
- optional("--barcode_type", barcode_type) +
- optional("--max_barcode_errors", max_barcode_errors) +
- optional("--phred_offset", phred_offset) +
+ optional("--last_bad_quality_char", lastBadQualityChar) +
+ optional("--barcode_type", barcodeType) +
+ optional("--max_barcode_errors", maxBarcodeErrors) +
+ optional("--phred_offset", phredOffset) +
(input match {
case l: List[_] if l.nonEmpty => required("-i", l.mkString(","))
case _ => ""
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
index 2f89774db..80e999db7 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
@@ -30,23 +30,23 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
@Output(doc = "Markdup output bam")
var output: File = _
- var remove_duplicates: Boolean = config("remove_duplicates", default = false)
+ var removeDuplicates: Boolean = config("remove_duplicates", default = false)
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
- val compression_level: Option[Int] = config("compression_level", default = 6)
- val hash_table_size: Option[Int] = config("hash-table-size", default = 262144)
- val overflow_list_size: Option[Int] = config("overflow-list-size", default = 200000)
- val io_buffer_size: Option[Int] = config("io-buffer-size", default = 128)
+ val compressionLevel: Option[Int] = config("compression_level", default = 6)
+ val hashTableSize: Option[Int] = config("hash-table-size", default = 262144)
+ val overflowListSize: Option[Int] = config("overflow-list-size", default = 200000)
+ val ioBufferSize: Option[Int] = config("io-buffer-size", default = 128)
/** Returns command to execute */
def cmdLine = required(executable) +
required("markdup") +
- conditional(remove_duplicates, "--remove-duplicates") +
+ conditional(removeDuplicates, "--remove-duplicates") +
optional("-t", nCoresRequest) +
- optional("-l", compression_level) +
- optional("--hash-table-size=", hash_table_size, spaceSeparated = false) +
- optional("--overflow-list-size=", overflow_list_size, spaceSeparated = false) +
- optional("--io-buffer-size=", io_buffer_size, spaceSeparated = false) +
+ optional("-l", compressionLevel) +
+ optional("--hash-table-size=", hashTableSize, spaceSeparated = false) +
+ optional("--overflow-list-size=", overflowListSize, spaceSeparated = false) +
+ optional("--io-buffer-size=", ioBufferSize, spaceSeparated = false) +
required(input) +
required(output)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
index 83464fa49..4cfb1bc99 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
@@ -31,13 +31,13 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
var output: File = _
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
- val compression_level: Option[Int] = config("compression_level", default = 6)
+ val compressionLevel: Option[Int] = config("compression_level", default = 6)
/** Returns command to execute */
def cmdLine = required(executable) +
required("merge") +
optional("-t", nCoresRequest) +
- optional("-l", compression_level) +
+ optional("-l", compressionLevel) +
required(output) +
repeat("", input)
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
index ca2470c60..d5f9245ee 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
@@ -33,7 +33,7 @@ class SambambaView(val root: Configurable) extends Sambamba {
var filter: Option[String] = _
val format: Option[String] = config("format", default = "bam")
val regions: Option[File] = config("regions")
- val compression_level: Option[Int] = config("compression_level", default = 6)
+ val compressionLevel: Option[Int] = config("compression_level", default = 6)
/** Returns command to execute */
def cmdLine = required(executable) +
@@ -42,7 +42,7 @@ class SambambaView(val root: Configurable) extends Sambamba {
optional("--nthreads", nCoresRequest) +
optional("--format", format.get) +
optional("--regions", regions) +
- optional("--compression-level", compression_level) +
+ optional("--compression-level", compressionLevel) +
required("--output-filename", output) +
required(input)
}
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
index 27b17496f..fe5952237 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
@@ -84,10 +84,10 @@ object SeqStat extends ToolCommand {
*/
def detectPhredEncoding(quals: mutable.ArrayBuffer[Long]): Unit = {
// substract 1 on high value, because we start from index 0
- val qual_low_boundery = quals.takeWhile(_ == 0).length
- val qual_high_boundery = quals.length - 1
+ val qualLowBoundery = quals.takeWhile(_ == 0).length
+ val qualHighBoundery = quals.length - 1
- (qual_low_boundery < 59, qual_high_boundery > 74) match {
+ (qualLowBoundery < 59, qualHighBoundery > 74) match {
case (false, true) => phredEncoding = Solexa
// TODO: check this later on
// complex case, we cannot tell wheter this is a sanger or solexa
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index f9f0fe472..50893046b 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -64,13 +64,13 @@ object VepNormalizer extends ToolCommand {
versionCheck(header)
logger.debug("VCF version OK")
logger.debug("Parsing header")
- val new_infos = parseCsq(header)
+ val newInfos = parseCsq(header)
header.setWriteCommandLine(true)
val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
setOutputFile(output).setReferenceDictionary(header.getSequenceDictionary)
build ())
- for (info <- new_infos) {
+ for (info <- newInfos) {
val tmpheaderline = new VCFInfoHeaderLine(info, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "A VEP annotation")
header.addMetaDataLine(tmpheaderline)
}
@@ -81,7 +81,7 @@ object VepNormalizer extends ToolCommand {
writer.writeHeader(header)
logger.debug("Wrote header to file")
- normalize(reader, writer, new_infos, commandArgs.mode, commandArgs.removeCSQ)
+ normalize(reader, writer, newInfos, commandArgs.mode, commandArgs.removeCSQ)
writer.close()
logger.debug("Closed writer")
reader.close()
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
index f128a6b42..65af6ae0e 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
@@ -39,20 +39,20 @@ class AnnotateVcfWithBedTest extends TestNGSuite with MockitoSugar with Matchers
val rand = new Random()
@Test def testOutputTypeVcf() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
+ val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeBcf() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
+ val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path, "-B", bed, "-f", "testing")
+ val tmpPath = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmpPath, "-B", bed, "-f", "testing")
main(arguments)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index a88dc561a..f4455ca6a 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -35,11 +35,11 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
Paths.get(getClass.getResource(p).toURI).toString
}
- val vepped_path = resourcePath("/VEP_oneline.vcf")
- val vepped = new File(vepped_path)
- val bam_path = resourcePath("/paired01.bam")
- val chrQ_path = resourcePath("/chrQ.vcf.gz")
- val chrQRef_path = resourcePath("/fake_chrQ.fa")
+ val veppedPath = resourcePath("/VEP_oneline.vcf")
+ val vepped = new File(veppedPath)
+ val bamPath = resourcePath("/paired01.bam")
+ val chrQPath = resourcePath("/chrQ.vcf.gz")
+ val chrQRefPath = resourcePath("/fake_chrQ.fa")
val bam = new File(resourcePath("/paired01.bam"))
val chrQ = new File(resourcePath("/chrQ.vcf.gz"))
val chrQRef = new File(resourcePath("/fake_chrQ.fa"))
@@ -50,7 +50,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
- val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
+ val arguments = Array("-V", chrQPath, "--outputVariants", tmppath, "--sampleName", "Sample_101", "--reference", chrQRefPath, "--outputName", "test")
main(arguments)
}
@@ -60,7 +60,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
- val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
+ val arguments = Array("-V", chrQPath, "--outputVariants", tmppath, "--bamFile", bamPath, "--sampleName", "Sample_101", "--reference", chrQRefPath, "--outputName", "test")
main(arguments)
}
@@ -70,7 +70,7 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
val tmppath = tmp.getAbsolutePath
tmp.deleteOnExit()
- val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Sample_101", "--reference", chrQRef_path, "--outputName", "test")
+ val arguments = Array("-V", chrQPath, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bamPath, "--sampleName", "Sample_101", "--reference", chrQRefPath, "--outputName", "test")
main(arguments)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
index 1ee6f38d3..7281e4dea 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
@@ -47,24 +47,24 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
@Test def testOutputTypeVcf() = {
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".vcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmpPath)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".vcf.gz")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmpPath)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp = File.createTempFile("CheckAllelesVcfInBam", ".bcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmp_path)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vcf, "-b", bam, "-s", "sample01", "-o", tmpPath)
main(arguments)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
index aac4cb6c7..411b632aa 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GvcfToBedTest.scala
@@ -27,7 +27,7 @@ class GvcfToBedTest extends TestNGSuite with Matchers with MockitoSugar {
val vepped = new File(resourcePath("/VEP_oneline.vcf"))
val unvepped = new File(resourcePath("/unvepped.vcf"))
- val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val veppedPath = resourcePath("/VEP_oneline.vcf")
@Test def testMinQuality = {
val reader = new VCFFileReader(vepped, false)
@@ -64,23 +64,23 @@ class GvcfToBedTest extends TestNGSuite with Matchers with MockitoSugar {
@Test
def testGvcfToBedInvertedOutput = {
val tmp = File.createTempFile("gvcf2bedtest", ".bed")
- val tmp_inv = File.createTempFile("gvcf2bedtest", ".bed")
+ val tmpInv = File.createTempFile("gvcf2bedtest", ".bed")
tmp.deleteOnExit()
- tmp_inv.deleteOnExit()
+ tmpInv.deleteOnExit()
val args: Array[String] = Array("-I", unvepped.getAbsolutePath, "-O", tmp.getAbsolutePath, "-S", "Sample_101",
- "--minGenomeQuality", "99", "--invertedOutputBed", tmp_inv.getAbsolutePath)
+ "--minGenomeQuality", "99", "--invertedOutputBed", tmpInv.getAbsolutePath)
main(args)
- Source.fromFile(tmp_inv).getLines().size shouldBe 1
+ Source.fromFile(tmpInv).getLines().size shouldBe 1
val tmp2 = File.createTempFile("gvcf2bedtest", ".bed")
- val tmp2_inv = File.createTempFile("gvcf2bedtest", ".bed")
+ val tmp2Inv = File.createTempFile("gvcf2bedtest", ".bed")
tmp2.deleteOnExit()
- tmp2_inv.deleteOnExit()
+ tmp2Inv.deleteOnExit()
val args2: Array[String] = Array("-I", unvepped.getAbsolutePath, "-O", tmp.getAbsolutePath, "-S", "Sample_102",
- "--minGenomeQuality", "3", "--invertedOutputBed", tmp2_inv.getAbsolutePath)
+ "--minGenomeQuality", "3", "--invertedOutputBed", tmp2Inv.getAbsolutePath)
main(args2)
- Source.fromFile(tmp2_inv).getLines().size shouldBe 0
+ Source.fromFile(tmp2Inv).getLines().size shouldBe 0
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
index b7ea9bb9c..538948557 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
@@ -51,24 +51,24 @@ class MergeAllelesTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testOutputTypeVcf() = {
val tmp = File.createTempFile("MergeAlleles", ".vcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
main(arguments)
}
@Test def testOutputTypeVcfGz() = {
val tmp = File.createTempFile("MergeAlleles", ".vcf.gz")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
main(arguments)
}
@Test def testOutputTypeBcf() = {
val tmp = File.createTempFile("MergeAlleles", ".bcf")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vepped_path, "-o", tmp_path, "-R", reference)
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vepped_path, "-o", tmpPath, "-R", reference)
main(arguments)
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
index 46e0ffa93..1406cef29 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
@@ -81,14 +81,14 @@ class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
for (record <- vcfReader) {
val alleles = record.getAlleles.toSet
- var ref_alleles = alleles -- record.getAlternateAlleles.toSet
+ var refAlleles = alleles -- record.getAlternateAlleles.toSet
- ref_alleles.size should be >= 1
+ refAlleles.size should be >= 1
val realRef = Allele.create(sequenceFile.getSubsequenceAt(record.getContig,
record.getStart, record.getEnd).getBases, true)
- for (ref <- ref_alleles) {
+ for (ref <- refAlleles) {
record.extraStrictValidation(ref, realRef, Set(""))
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
index a53c4dd31..e791d8093 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -77,13 +77,13 @@ class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
val line = values.head._2.keys.map(x => createLine(paths, values, x)).head
line should equal("value\t")
- val sample_values = fetchValues(summary, paths, true, false)
- val sample_line = sample_values.head._2.keys.map(x => createLine(paths, sample_values, x)).head
- sample_line should equal("016\t")
+ val sampleValues = fetchValues(summary, paths, true, false)
+ val sampleLine = sampleValues.head._2.keys.map(x => createLine(paths, sampleValues, x)).head
+ sampleLine should equal("016\t")
- val lib_values = fetchValues(summary, paths, false, true)
- val lib_line = lib_values.head._2.keys.map(x => createLine(paths, lib_values, x)).head
- lib_line should equal("016-L001\tfalse")
+ val libValues = fetchValues(summary, paths, false, true)
+ val libLine = libValues.head._2.keys.map(x => createLine(paths, libValues, x)).head
+ libLine should equal("016-L001\tfalse")
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
index ee327392c..76379526a 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
@@ -44,31 +44,31 @@ class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testAllFields() = {
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", unvepped, "-o", tmp_path, "--all_info")
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", unvepped, "-o", tmpPath, "--all_info")
main(arguments)
}
@Test def testSpecificField() = {
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vepped, "-o", tmp_path, "-i", "CSQ")
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vepped, "-o", tmpPath, "-i", "CSQ")
main(arguments)
}
@Test def testNewSeparators() = {
val tmp = File.createTempFile("VcfToTsv", ".tsv")
tmp.deleteOnExit()
- val tmp_path = tmp.getAbsolutePath
- val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",", "--list_separator", "|")
+ val tmpPath = tmp.getAbsolutePath
+ val arguments = Array("-I", vepped, "-o", tmpPath, "--all_info", "--separator", ",", "--list_separator", "|")
main(arguments)
}
@Test(expectedExceptions = Array(classOf[IllegalArgumentException]))
def testIdenticalSeparators() = {
- val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
- val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",")
+ val tmpPath = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmpPath, "--all_info", "--separator", ",")
main(arguments)
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index a6a708810..2f1814210 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -105,7 +105,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
@Test
def testFieldMap = {
- val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
+ val unvepRecord = new VCFFileReader(new File(unveppedPath)).iterator().next()
var fields = List(new Fields("FG", "FG"))
fields :::= List(new Fields("FD", "FD"))
@@ -133,7 +133,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
fields :::= List(new Fields("VQSLOD", "VQSLOD"))
fields :::= List(new Fields("culprit", "culprit"))
- val fieldMap = createFieldMap(fields, List(unvep_record))
+ val fieldMap = createFieldMap(fields, List(unvepRecord))
fieldMap("FG") shouldBe List("intron")
fieldMap("FD") shouldBe List("unknown")
@@ -163,26 +163,26 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test def testGetSecondaryRecords = {
- val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
- val vep_reader = new VCFFileReader(new File(veppedPath))
- val vep_record = vep_reader.iterator().next()
+ val unvepRecord = new VCFFileReader(new File(unveppedPath)).iterator().next()
+ val vepReader = new VCFFileReader(new File(veppedPath))
+ val vepRecord = vepReader.iterator().next()
- val secRec = getSecondaryRecords(vep_reader, unvep_record, false)
+ val secRec = getSecondaryRecords(vepReader, unvepRecord, false)
- secRec.foreach(x => identicalVariantContext(x, vep_record) shouldBe true)
+ secRec.foreach(x => identicalVariantContext(x, vepRecord) shouldBe true)
}
@Test def testCreateRecord = {
- val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
- val vep_reader = new VCFFileReader(new File(veppedPath))
- val header = vep_reader.getFileHeader
- val vep_record = vep_reader.iterator().next()
+ val unvepRecord = new VCFFileReader(new File(unveppedPath)).iterator().next()
+ val vepReader = new VCFFileReader(new File(veppedPath))
+ val header = vepReader.getFileHeader
+ val vepRecord = vepReader.iterator().next()
- val secRec = getSecondaryRecords(vep_reader, unvep_record, false)
+ val secRec = getSecondaryRecords(vepReader, unvepRecord, false)
val fieldMap = createFieldMap(List(new Fields("CSQ", "CSQ")), secRec)
- val created_record = createRecord(fieldMap, unvep_record, List(new Fields("CSQ", "CSQ")), header)
- identicalVariantContext(created_record, vep_record) shouldBe true
+ val createdRecord = createRecord(fieldMap, unvepRecord, List(new Fields("CSQ", "CSQ")), header)
+ identicalVariantContext(createdRecord, vepRecord) shouldBe true
}
}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index 53aeddfaf..d84db877f 100644
--- a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -42,49 +42,49 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val vepped = new File(resourcePath("/VEP_oneline.vcf"))
val unvepped = new File(resourcePath("/unvepped.vcf"))
- val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val veppedPath = resourcePath("/VEP_oneline.vcf")
val rand = new Random()
@Test def testGzOutputExplode(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testVcfOutputExplode(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testBcfOutputExplode(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "explode")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "explode")
main(arguments)
}
@Test def testGzOutputStandard(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".vcf.gz")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testVcfOutputStandard(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".vcf")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@Test def testBcfOutputStandard(): Unit = {
val tmpFile = File.createTempFile("VepNormalizer_", ".bcf")
tmpFile.deleteOnExit()
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpFile.getAbsolutePath, "-m", "standard")
+ val arguments: Array[String] = Array("-I", veppedPath, "-O", tmpFile.getAbsolutePath, "-m", "standard")
main(arguments)
}
@@ -97,22 +97,22 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testExplodeVEPLength() = {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
- val new_infos = parseCsq(header)
- explodeTranscripts(reader.iterator().next(), new_infos, removeCsq = true).length should be(11)
+ val newInfos = parseCsq(header)
+ explodeTranscripts(reader.iterator().next(), newInfos, removeCsq = true).length should be(11)
}
@Test def testStandardVEPLength() = {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
- val new_infos = parseCsq(header)
- Array(standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)).length should be(1)
+ val newInfos = parseCsq(header)
+ Array(standardTranscripts(reader.iterator().next(), newInfos, removeCsq = true)).length should be(1)
}
@Test def testStandardVEPAttributeLength() = {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
- val new_infos = parseCsq(header)
- val record = standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)
+ val newInfos = parseCsq(header)
+ val record = standardTranscripts(reader.iterator().next(), newInfos, removeCsq = true)
def checkItems(items: Array[String]) = {
items.foreach { check }
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 83bde757c..5dd4dd9aa 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -28,7 +28,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def this() = this(null)
@Input(doc = "R1 fastq file (gzipped allowed)", shortName = "R1", required = true)
- var input_R1: File = _
+ var inputR1: File = _
@Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", required = false)
var input_R2: Option[File] = None
@@ -47,7 +47,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Returns files to store in summary */
def summaryFiles: Map[String, File] = {
- Map("input_R1" -> input_R1, "output_R1" -> fastqR1Qc) ++
+ Map("input_R1" -> inputR1, "output_R1" -> fastqR1Qc) ++
(if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> fastqR2Qc.get) else Map())
}
@@ -55,13 +55,13 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
var paired: Boolean = input_R2.isDefined
- var R1_name: String = _
- var R2_name: String = _
+ var R1Name: String = _
+ var R2Name: String = _
- var fastqc_R1: Fastqc = _
- var fastqc_R2: Fastqc = _
- var fastqc_R1_after: Fastqc = _
- var fastqc_R2_after: Fastqc = _
+ var fastqcR1: Fastqc = _
+ var fastqcR2: Fastqc = _
+ var fastqcR1After: Fastqc = _
+ var fastqcR2After: Fastqc = _
override def reportClass = {
val flexiprepReport = new FlexiprepReport(this)
@@ -76,19 +76,19 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Function that's need to be executed before the script is accessed */
def init() {
require(outputDir != null, "Missing output directory on flexiprep module")
- require(input_R1 != null, "Missing input R1 on flexiprep module")
+ require(inputR1 != null, "Missing input R1 on flexiprep module")
require(sampleId != null, "Missing sample ID on flexiprep module")
require(libId != null, "Missing library ID on flexiprep module")
paired = input_R2.isDefined
- inputFiles :+= new InputFile(input_R1)
+ inputFiles :+= new InputFile(inputR1)
input_R2.foreach(inputFiles :+= new InputFile(_))
- R1_name = getUncompressedFileName(input_R1)
+ R1Name = getUncompressedFileName(inputR1)
input_R2.foreach { fileR2 =>
paired = true
- R2_name = getUncompressedFileName(fileR2)
+ R2Name = getUncompressedFileName(fileR2)
}
}
@@ -96,26 +96,26 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def biopetScript() {
runInitialJobs()
- if (paired) runTrimClip(input_R1, input_R2, outputDir)
- else runTrimClip(input_R1, outputDir)
+ if (paired) runTrimClip(inputR1, input_R2, outputDir)
+ else runTrimClip(inputR1, outputDir)
- val R1_files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
- val R2_files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
- runFinalize(R1_files.toList, R2_files.toList)
+ val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
+ val R2Files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
+ runFinalize(R1Files.toList, R2Files.toList)
}
/** Add init non chunkable jobs */
def runInitialJobs() {
- outputFiles += ("fastq_input_R1" -> input_R1)
+ outputFiles += ("fastq_input_R1" -> inputR1)
if (paired) outputFiles += ("fastq_input_R2" -> input_R2.get)
- fastqc_R1 = Fastqc(this, input_R1, new File(outputDir, R1_name + ".fastqc/"))
- add(fastqc_R1)
- addSummarizable(fastqc_R1, "fastqc_R1")
- outputFiles += ("fastqc_R1" -> fastqc_R1.output)
+ fastqcR1 = Fastqc(this, inputR1, new File(outputDir, R1Name + ".fastqc/"))
+ add(fastqcR1)
+ addSummarizable(fastqcR1, "fastqc_R1")
+ outputFiles += ("fastqc_R1" -> fastqcR1.output)
val validateFastq = new ValidateFastq(this)
- validateFastq.r1Fastq = input_R1
+ validateFastq.r1Fastq = inputR1
validateFastq.r2Fastq = input_R2
validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
add(validateFastq)
@@ -128,22 +128,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
if (paired) {
- fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
- add(fastqc_R2)
- addSummarizable(fastqc_R2, "fastqc_R2")
- outputFiles += ("fastqc_R2" -> fastqc_R2.output)
+ fastqcR2 = Fastqc(this, input_R2.get, new File(outputDir, R2Name + ".fastqc/"))
+ add(fastqcR2)
+ addSummarizable(fastqcR2, "fastqc_R2")
+ outputFiles += ("fastqc_R2" -> fastqcR2.output)
}
- val seqstat_R1 = SeqStat(this, input_R1, outputDir)
- seqstat_R1.isIntermediate = true
- add(seqstat_R1)
- addSummarizable(seqstat_R1, "seqstat_R1")
+ val seqstatR1 = SeqStat(this, inputR1, outputDir)
+ seqstatR1.isIntermediate = true
+ add(seqstatR1)
+ addSummarizable(seqstatR1, "seqstat_R1")
if (paired) {
- val seqstat_R2 = SeqStat(this, input_R2.get, outputDir)
- seqstat_R2.isIntermediate = true
- add(seqstat_R2)
- addSummarizable(seqstat_R2, "seqstat_R2")
+ val seqstatR2 = SeqStat(this, input_R2.get, outputDir)
+ seqstatR2.isIntermediate = true
+ add(seqstatR2)
+ addSummarizable(seqstatR2, "seqstat_R2")
}
}
@@ -176,17 +176,17 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var R1 = R1_in
var R2 = R2_in
- val qcCmdR1 = new QcCommand(this, fastqc_R1)
+ val qcCmdR1 = new QcCommand(this, fastqcR1)
qcCmdR1.input = R1_in
qcCmdR1.read = "R1"
qcCmdR1.output = if (paired) new File(outDir, fastqR1Qc.getName.stripSuffix(".gz"))
else fastqR1Qc
- qcCmdR1.deps :+= fastqc_R1.output
+ qcCmdR1.deps :+= fastqcR1.output
qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
addSummarizable(qcCmdR1, "qc_command_R1")
if (paired) {
- val qcCmdR2 = new QcCommand(this, fastqc_R2)
+ val qcCmdR2 = new QcCommand(this, fastqcR2)
qcCmdR2.input = R2_in.get
qcCmdR2.output = new File(outDir, fastqR2Qc.get.getName.stripSuffix(".gz"))
qcCmdR2.read = "R2"
@@ -222,8 +222,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
}
- pipe.deps ::= fastqc_R1.output
- pipe.deps ::= fastqc_R2.output
+ pipe.deps ::= fastqcR1.output
+ pipe.deps ::= fastqcR2.output
pipe.isIntermediate = !keepQcFastqFiles
add(pipe)
@@ -236,14 +236,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
R1 = qcCmdR1.output
}
- val seqstat_R1_after = SeqStat(this, R1, outDir)
- add(seqstat_R1_after)
- addSummarizable(seqstat_R1_after, "seqstat_R1_qc")
+ val seqstatR1After = SeqStat(this, R1, outDir)
+ add(seqstatR1After)
+ addSummarizable(seqstatR1After, "seqstat_R1_qc")
if (paired) {
- val seqstat_R2_after = SeqStat(this, R2.get, outDir)
- add(seqstat_R2_after)
- addSummarizable(seqstat_R2_after, "seqstat_R2_qc")
+ val seqstatR2After = SeqStat(this, R2.get, outDir)
+ add(seqstatR2After)
+ addSummarizable(seqstatR2After, "seqstat_R2_qc")
}
outputFiles += (chunk + "output_R1" -> R1)
@@ -283,14 +283,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += ("output_R1_gzip" -> fastqR1Qc)
if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
- fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
- add(fastqc_R1_after)
- addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
+ fastqcR1After = Fastqc(this, fastqR1Qc, new File(outputDir, R1Name + ".qc.fastqc/"))
+ add(fastqcR1After)
+ addSummarizable(fastqcR1After, "fastqc_R1_qc")
if (paired) {
- fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
- add(fastqc_R2_after)
- addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
+ fastqcR2After = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2Name + ".qc.fastqc/"))
+ add(fastqcR2After)
+ addSummarizable(fastqcR2After, "fastqc_R2_qc")
}
addSummaryJobs()
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 2b0593382..5d92bf92b 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -115,18 +115,18 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
trim = if (!flexiprep.skipTrim) {
val sickle = new Sickle(root)
- sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
- sickle.input_R1 = clip match {
+ sickle.outputStats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
+ sickle.inputR1 = clip match {
case Some(c) => c.fastqOutput
case _ => seqtk.output
}
- sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
+ sickle.outputR1 = new File(output.getParentFile, input.getName + ".sickle.fq")
addPipeJob(sickle)
Some(sickle)
} else None
val outputFile = (clip, trim) match {
- case (_, Some(t)) => t.output_R1
+ case (_, Some(t)) => t.outputR1
case (Some(c), _) => c.fastqOutput
case _ => seqtk.output
}
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 891d32ae3..f4b671894 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -70,7 +70,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
), Map(FlexiprepTest.executables.toSeq: _*))
val flexiprep: Flexiprep = initPipeline(map)
- flexiprep.input_R1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
+ flexiprep.inputR1 = (if (zipped) FlexiprepTest.r1Zipped else FlexiprepTest.r1)
if (paired) flexiprep.input_R2 = Some((if (zipped) FlexiprepTest.r2Zipped else FlexiprepTest.r2))
flexiprep.sampleId = Some("1")
flexiprep.libId = Some("1")
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 37c6f110a..d3c94062c 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -97,7 +97,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
lazy val flexiprep = new Flexiprep(qscript)
flexiprep.sampleId = Some(sampleId)
flexiprep.libId = Some(libId)
- flexiprep.input_R1 = config("R1")
+ flexiprep.inputR1 = config("R1")
flexiprep.input_R2 = config("R2")
flexiprep.outputDir = new File(libDir, "flexiprep")
@@ -108,7 +108,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */
protected def addJobs(): Unit = {
- inputFiles :+= InputFile(flexiprep.input_R1, config("R1_md5"))
+ inputFiles :+= InputFile(flexiprep.inputR1, config("R1_md5"))
flexiprep.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
add(flexiprep)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
index 3e1a7b48d..e21645fba 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
@@ -58,18 +58,18 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
krakenAnalysis.paired = fastqR2.isDefined
- krakenAnalysis.classified_out = Some(new File(outputDir, s"$outputName.krkn.classified.fastq"))
- krakenAnalysis.unclassified_out = Some(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
+ krakenAnalysis.classifiedOut = Some(new File(outputDir, s"$outputName.krkn.classified.fastq"))
+ krakenAnalysis.unclassifiedOut = Some(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
add(krakenAnalysis)
outputFiles += ("kraken_output_raw" -> krakenAnalysis.output)
- outputFiles += ("kraken_classified_out" -> krakenAnalysis.classified_out.getOrElse(""))
- outputFiles += ("kraken_unclassified_out" -> krakenAnalysis.unclassified_out.getOrElse(""))
+ outputFiles += ("kraken_classified_out" -> krakenAnalysis.classifiedOut.getOrElse(""))
+ outputFiles += ("kraken_unclassified_out" -> krakenAnalysis.unclassifiedOut.getOrElse(""))
// create kraken summary file
val krakenReport = new KrakenReport(this)
krakenReport.input = krakenAnalysis.output
- krakenReport.show_zeros = true
+ krakenReport.showZeros = true
krakenReport.output = new File(outputDir, s"$outputName.krkn.full")
add(krakenReport)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
index 7fa102d11..4076479ba 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
@@ -42,7 +42,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
val splitLib = new SplitLibrariesFastq(this)
splitLib.input :+= fastqInput
splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
- sampleId.foreach(splitLib.sample_ids :+= _)
+ sampleId.foreach(splitLib.sampleIds :+= _)
add(splitLib)
val closedReference = new PickClosedReferenceOtus(this)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
index f50a38a86..d893d071f 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala
@@ -45,14 +45,14 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
val slfR1 = new SplitLibrariesFastq(this)
slfR1.input :+= fastqR1
slfR1.outputDir = new File(outputDir, "split_libraries_fastq_R1")
- sampleId.foreach(slfR1.sample_ids :+= _)
+ sampleId.foreach(slfR1.sampleIds :+= _)
add(slfR1)
lazy val slfR2 = fastqR2.map { file =>
val j = new SplitLibrariesFastq(this)
j.input :+= file
j.outputDir = new File(outputDir, "split_libraries_fastq_R2")
- sampleId.foreach(j.sample_ids :+= _)
+ sampleId.foreach(j.sampleIds :+= _)
add(j)
j
}
@@ -75,8 +75,8 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
assignTaxonomy.outputDir = new File(outputDir, "assign_taxonomy")
assignTaxonomy.jobOutputFile = new File(assignTaxonomy.outputDir, ".assign_taxonomy.out")
assignTaxonomy.inputFasta = pickRepSet.outputFasta.get
- assignTaxonomy.read_1_seqs_fp = Some(slfR1.outputSeqs)
- assignTaxonomy.read_2_seqs_fp = slfR2.map(_.outputSeqs)
+ assignTaxonomy.read1SeqsFp = Some(slfR1.outputSeqs)
+ assignTaxonomy.read2SeqsFp = slfR2.map(_.outputSeqs)
add(assignTaxonomy)
}
}
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index abe9edf5a..972307ed7 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -79,7 +79,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
protected def executeFlexiprep(r1: File, r2: Option[File]): (File, Option[File]) = {
if (!skipFlexiprep) {
val flexiprep = new Flexiprep(this)
- flexiprep.input_R1 = r1
+ flexiprep.inputR1 = r1
flexiprep.input_R2 = r2
flexiprep.outputDir = new File(outputDir, "flexiprep")
add(flexiprep)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index adee53966..37f3cf7a4 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -215,10 +215,10 @@ class Gentrap(val root: Configurable) extends QScript
} else bamFile
/** Whether all libraries are paired or not */
- def allPaired: Boolean = libraries.values.forall(_.mapping.forall(_.input_R2.isDefined))
+ def allPaired: Boolean = libraries.values.forall(_.mapping.forall(_.inputR2.isDefined))
/** Whether all libraries are single or not */
- def allSingle: Boolean = libraries.values.forall(_.mapping.forall(_.input_R2.isEmpty))
+ def allSingle: Boolean = libraries.values.forall(_.mapping.forall(_.inputR2.isEmpty))
/** Adds all jobs for the sample */
override def addJobs(): Unit = {
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
index 30bdcb589..c3af9880e 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.queue.QScript
class CufflinksGuided(val root: Configurable) extends QScript with CufflinksMeasurement with AnnotationGtf {
override def makeCufflinksJob(id: String, bamFile: File) = {
val cufflinks = super.makeCufflinksJob(id, bamFile)
- cufflinks.GTF_guide = Some(annotationGtf)
+ cufflinks.gtfGuide = Some(annotationGtf)
cufflinks
}
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
index 26616991e..b3410cd9d 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
@@ -11,7 +11,7 @@ trait CufflinksMeasurement extends QScript with Measurement {
def makeCufflinksJob(id: String, bamFile: File) = {
val cufflinks = new Cufflinks(this)
cufflinks.input = bamFile
- cufflinks.output_dir = new File(outputDir, id)
+ cufflinks.outputDir = new File(outputDir, id)
cufflinks
}
@@ -25,14 +25,14 @@ trait CufflinksMeasurement extends QScript with Measurement {
val genesFpkmFiles = jobs.toList.map {
case (id, job) =>
- val file = new File(job.output_dir, s"$id.genes_fpkm.counts")
+ val file = new File(job.outputDir, s"$id.genes_fpkm.counts")
add(Ln(this, job.outputGenesFpkm, file))
file
}
val isoFormFpkmFiles = jobs.toList.map {
case (id, job) =>
- val file = new File(job.output_dir, s"$id.iso_form_fpkn.counts")
+ val file = new File(job.outputDir, s"$id.iso_form_fpkn.counts")
add(Ln(this, job.outputIsoformsFpkm, file))
file
}
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index d37f8031b..ed509aee9 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -42,10 +42,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def this() = this(null)
@Input(doc = "R1 fastq file", shortName = "R1", required = true)
- var input_R1: File = _
+ var inputR1: File = _
@Input(doc = "R2 fastq file", shortName = "R2", required = false)
- var input_R2: Option[File] = None
+ var inputR2: Option[File] = None
/** Output name */
var outputName: String = _
@@ -107,9 +107,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
)
/** File to add to the summary */
- def summaryFiles: Map[String, File] = Map("output_bam" -> finalBamFile, "input_R1" -> input_R1,
+ def summaryFiles: Map[String, File] = Map("output_bam" -> finalBamFile, "input_R1" -> inputR1,
"reference" -> referenceFasta()) ++
- (if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
+ (if (inputR2.isDefined) Map("input_R2" -> inputR2.get) else Map())
/** Settings to add to summary */
def summarySettings = Map(
@@ -134,14 +134,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Will be executed before script */
def init() {
require(outputDir != null, "Missing output directory on mapping module")
- require(input_R1 != null, "Missing output directory on mapping module")
+ require(inputR1 != null, "Missing output directory on mapping module")
require(sampleId.isDefined, "Missing sample ID on mapping module")
require(libId.isDefined, "Missing library ID on mapping module")
- inputFiles :+= new InputFile(input_R1)
- input_R2.foreach(inputFiles :+= new InputFile(_))
+ inputFiles :+= new InputFile(inputR1)
+ inputR2.foreach(inputFiles :+= new InputFile(_))
- paired = input_R2.isDefined
+ paired = inputR2.isDefined
if (readgroupId == null)
readgroupId = config("readgroup_id", default = sampleId.get + "-" + libId.get)
@@ -153,8 +153,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
else {
val chunkSize: Int = config("chunksize", 1 << 30)
- val filesize = if (input_R1.getName.endsWith(".gz") || input_R1.getName.endsWith(".gzip")) input_R1.length * 3
- else input_R1.length
+ val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3
+ else inputR1.length
numberChunks = Option(ceil(filesize.toDouble / chunkSize).toInt)
}
}
@@ -166,40 +166,40 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def biopetScript() {
if (!skipFlexiprep) {
flexiprep.outputDir = new File(outputDir, "flexiprep")
- flexiprep.input_R1 = input_R1
- flexiprep.input_R2 = input_R2
+ flexiprep.inputR1 = inputR1
+ flexiprep.input_R2 = inputR2
flexiprep.sampleId = this.sampleId
flexiprep.libId = this.libId
flexiprep.init()
flexiprep.runInitialJobs()
}
var bamFiles: List[File] = Nil
- var fastq_R1_output: List[File] = Nil
- var fastq_R2_output: List[File] = Nil
+ var fastqR1Output: List[File] = Nil
+ var fastqR2Output: List[File] = Nil
val chunks: Map[File, (File, Option[File])] = {
if (chunking) (for (t <- 1 to numberChunks.getOrElse(1)) yield {
val chunkDir = new File(outputDir, "chunks" + File.separator + t)
- chunkDir -> (new File(chunkDir, input_R1.getName),
- if (paired) Some(new File(chunkDir, input_R2.get.getName)) else None)
+ chunkDir -> (new File(chunkDir, inputR1.getName),
+ if (paired) Some(new File(chunkDir, inputR2.get.getName)) else None)
}).toMap
- else if (skipFlexiprep) Map(outputDir -> (input_R1, if (paired) input_R2 else None))
- else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
+ else if (skipFlexiprep) Map(outputDir -> (inputR1, if (paired) inputR2 else None))
+ else Map(outputDir -> (flexiprep.inputR1, flexiprep.input_R2))
}
if (chunking) {
- val fastSplitter_R1 = new FastqSplitter(this)
- fastSplitter_R1.input = input_R1
- for ((chunkDir, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
- fastSplitter_R1.isIntermediate = true
- add(fastSplitter_R1)
+ val fastSplitterR1 = new FastqSplitter(this)
+ fastSplitterR1.input = inputR1
+ for ((chunkDir, fastqfile) <- chunks) fastSplitterR1.output :+= fastqfile._1
+ fastSplitterR1.isIntermediate = true
+ add(fastSplitterR1)
if (paired) {
- val fastSplitter_R2 = new FastqSplitter(this)
- fastSplitter_R2.input = input_R2.get
- for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2.get
- fastSplitter_R2.isIntermediate = true
- add(fastSplitter_R2)
+ val fastSplitterR2 = new FastqSplitter(this)
+ fastSplitterR2.input = inputR2.get
+ for ((chunkDir, fastqfile) <- chunks) fastSplitterR2.output :+= fastqfile._2.get
+ fastSplitterR2.isIntermediate = true
+ add(fastSplitterR2)
}
}
@@ -211,8 +211,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
- fastq_R1_output :+= R1
- R2.foreach(R2 => fastq_R2_output :+= R2)
+ fastqR1Output :+= R1
+ R2.foreach(R2 => fastqR2Output :+= R2)
}
val outputBam = new File(chunkDir, outputName + ".bam")
@@ -234,7 +234,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
addAll(BamMetrics(this, outputBam, new File(chunkDir, "metrics"), sampleId, libId).functions)
}
if (!skipFlexiprep) {
- flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
+ flexiprep.runFinalize(fastqR1Output, fastqR2Output)
addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
addSummaryQScript(flexiprep)
}
@@ -356,15 +356,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val tophat = new Tophat(this)
tophat.R1 = tophat.R1 :+ R1
if (paired) tophat.R2 = tophat.R2 :+ R2.get
- tophat.output_dir = new File(outputDir, "tophat_out")
+ tophat.outputDir = new File(outputDir, "tophat_out")
// always output BAM
- tophat.no_convert_bam = false
+ tophat.noConvertBam = false
// and always keep input ordering
- tophat.keep_fasta_order = true
+ tophat.keepFastaOrder = true
add(tophat)
// fix unmapped file coordinates
- val fixedUnmapped = new File(tophat.output_dir, "unmapped_fixup.sam")
+ val fixedUnmapped = new File(tophat.outputDir, "unmapped_fixup.sam")
val fixer = new TophatRecondition(this)
fixer.inputBam = tophat.outputAcceptedHits
fixer.outputSam = fixedUnmapped.getAbsoluteFile
@@ -372,14 +372,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add(fixer)
// sort fixed SAM file
- val sorter = SortSam(this, fixer.outputSam, new File(tophat.output_dir, "unmapped_fixup.sorted.bam"))
+ val sorter = SortSam(this, fixer.outputSam, new File(tophat.outputDir, "unmapped_fixup.sorted.bam"))
sorter.sortOrder = "coordinate"
sorter.isIntermediate = true
add(sorter)
// merge with mapped file
val mergeSamFile = MergeSamFiles(this, List(tophat.outputAcceptedHits, sorter.output),
- new File(tophat.output_dir, "fixed_merged.bam"), sortOrder = "coordinate")
+ new File(tophat.outputDir, "fixed_merged.bam"), sortOrder = "coordinate")
mergeSamFile.createIndex = true
mergeSamFile.isIntermediate = true
add(mergeSamFile)
@@ -443,7 +443,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Add bowtie2 jobs **/
def addBowtie2(R1: File, R2: Option[File], output: File): File = {
val bowtie2 = new Bowtie2(this)
- bowtie2.rg_id = Some(readgroupId)
+ bowtie2.rgId = Some(readgroupId)
bowtie2.rg +:= ("LB:" + libId.get)
bowtie2.rg +:= ("PL:" + platform)
bowtie2.rg +:= ("PU:" + platformUnit)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
index a69160a6a..5f69fc45e 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
@@ -110,8 +110,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
if (inputR1.isDefined) {
mapping.foreach { m =>
- m.input_R1 = inputR1.get
- m.input_R2 = inputR2
+ m.inputR1 = inputR1.get
+ m.inputR2 = inputR2
add(m)
}
} else if (inputBam.isDefined) {
@@ -122,8 +122,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
samToFastq.isIntermediate = libraries.size > 1
qscript.add(samToFastq)
mapping.foreach(m => {
- m.input_R1 = samToFastq.fastqR1
- m.input_R2 = Some(samToFastq.fastqR2)
+ m.inputR1 = samToFastq.fastqR1
+ m.inputR2 = Some(samToFastq.fastqR2)
add(m)
})
} else {
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 7af4c60d5..cce528aaa 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -73,11 +73,11 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
val mapping: Mapping = initPipeline(map)
if (zipped) {
- mapping.input_R1 = r1Zipped
- if (paired) mapping.input_R2 = Some(r2Zipped)
+ mapping.inputR1 = r1Zipped
+ if (paired) mapping.inputR2 = Some(r2Zipped)
} else {
- mapping.input_R1 = r1
- if (paired) mapping.input_R2 = Some(r2)
+ mapping.inputR1 = r1
+ if (paired) mapping.inputR2 = Some(r2)
}
mapping.sampleId = Some("1")
mapping.libId = Some("1")
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 8d28a6ea1..3ef45bc4e 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -92,7 +92,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
inputFiles :+= new InputFile(inputFastq, config("R1_md5"))
flexiprep.outputDir = new File(libDir, "flexiprep/")
- flexiprep.input_R1 = inputFastq
+ flexiprep.inputR1 = inputFastq
flexiprep.init()
flexiprep.biopetScript()
qscript.addAll(flexiprep.functions)
@@ -105,7 +105,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
pf.deps +:= flexiprep.outputFiles("fastq_input_R1")
qscript.add(pf)
- mapping.input_R1 = pf.outputFastq
+ mapping.inputR1 = pf.outputFastq
mapping.outputDir = libDir
mapping.init()
mapping.biopetScript()
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index 506aed383..25281ec11 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -36,11 +36,11 @@ class Pindel(val root: Configurable) extends SvCaller {
for ((sample, bamFile) <- inputBams) {
val pindelDir = new File(outputDir, sample)
- val config_file: File = new File(pindelDir, sample + ".pindel.cfg")
+ val configFile: File = new File(pindelDir, sample + ".pindel.cfg")
val cfg = new PindelConfig(this)
cfg.input = bamFile
cfg.sampleName = sample
- cfg.output = config_file
+ cfg.output = configFile
add(cfg)
val pindel = PindelCaller(this, cfg.output, pindelDir)
--
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