diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
new file mode 100644
index 0000000000000000000000000000000000000000..286b7235b4e3ab8bccb0e3fbb19f752ef9cfc93f
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
@@ -0,0 +1,121 @@
+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author Wibowo Arindrarto
+ */
+
+package nl.lumc.sasc.biopet.function
+
+import java.io.File
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+/**
+ * Abstract class for all seqtk wrappers.
+ */
+abstract class Seqtk extends BiopetCommandLineFunction {
+ executable = config("exe", default = "seqtk", submodule = "seqtk")
+ override def versionCommand = executable
+ override val versionRegex = """Version: (.*)""".r
+}
+
+/**
+ * Wrapper for the seqtk seq subcommand.
+ * Written based on seqtk version 1.0-r63-dirty.
+ */
+class SeqtkSeq(val root: Configurable) extends Seqtk {
+
+ /** input file */
+ @Input(doc = "Input file (FASTQ or FASTA)")
+ var input: File = _
+
+ /** output file */
+ @Output(doc = "Output file")
+ var output: File = _
+
+ /** mask bases with quality lower than INT [0] */
+ var q: Option[Int] = config("q")
+
+ /** masked bases converted to CHAR; 0 for lowercase [0] */
+ var n: String = config("n")
+
+ /** number of residues per line; 0 for 2^32-1 [0] */
+ var l: Option[Int] = config("l")
+
+ /** quality shift: ASCII-INT gives base quality [33] */
+ var Q: Option[Int] = config("Q")
+
+ /** random seed (effective with -f) [11] */
+ var s: Option[Int] = config("s")
+
+ /** sample FLOAT fraction of sequences [1] */
+ var f: Option[Int] = config("f")
+
+ /** mask regions in BED or name list FILE [null] */
+ var M: File = config("M")
+
+ /** drop sequences with length shorter than INT [0] */
+ var L: Option[Int] = config("L")
+
+ /** mask complement region (effective with -M) */
+ var c: Boolean = config("c")
+
+ /** reverse complement */
+ var r: Boolean = config("r")
+
+ /** force FASTA output (discard quality) */
+ var A: Boolean = config("A")
+
+ /** drop comments at the header lines */
+ var C: Boolean = config("C")
+
+ /** drop sequences containing ambiguous bases */
+ var N: Boolean = config("N")
+
+ /** output the 2n-1 reads only */
+ var flag1: Boolean = config("1")
+
+ /** output the 2n reads only */
+ var flag2: Boolean = config("2")
+
+ /** shift quality by '(-Q) - 33' */
+ var V: Boolean = config("V")
+
+ def cmdLine = {
+ required(executable) +
+ " seq " +
+ optional("-q", q) +
+ optional("-n", n) +
+ optional("-l", l) +
+ optional("-Q", Q) +
+ optional("-s", s) +
+ optional("-f", f) +
+ optional("-M", M) +
+ optional("-L", L) +
+ conditional(c, "-c") +
+ conditional(r, "-r") +
+ conditional(A, "-A") +
+ conditional(C, "-C") +
+ conditional(N, "-N") +
+ conditional(flag1, "-1") +
+ conditional(flag2, "-2") +
+ conditional(V, "-V") +
+ required(input) +
+ " > " + required(output)
+ }
+
+ /**
+ * Calculates the offset required for the -Q flag for format conversion (-V flag set).
+ * This is required since seqtk computes the encoding offset indirectly from the input
+ * and output offsets.
+ *
+ * @param inQualOffset ASCII offset of the input file encoding
+ * @param outQualOffset ASCII offset of the output file encoding
+ * @return the value to be used with the -Q flag with -V set
+ */
+ def calcQForV(inQualOffset: Int, outQualOffset: Int): Int = {
+ // For the input for the -Q flag for seqtk, together with -V
+ inQualOffset - (outQualOffset - 33)
+ }
+}
diff --git a/extras/git.pre-commit b/extras/git.pre-commit
new file mode 100755
index 0000000000000000000000000000000000000000..5a627198950f191e4c2c64fe44d23cf170cfcf50
--- /dev/null
+++ b/extras/git.pre-commit
@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+
+# Adapted from: http://tech.yipit.com/2011/11/16/183772396/
+# Changes by Wibowo Arindrarto
+# Changes:
+# - Allow code modification by linters to be comitted
+# - Updated CHECKS
+# - Python 3 calls + code style updates
+#
+# Usage: save this file into your .git/hooks directory as `pre-commit`
+# and set it to executable
+
+import os
+import re
+import subprocess
+import sys
+
+modified = re.compile(r"^[MA]\s+(?P<name>.*)$")
+
+CHECKS = [
+ {
+ "exe": "scalariform",
+ "output": "Formatting code with scalariform ...",
+ # Remove lines without filenames
+ "command": "scalariform -s=2.11.1 -p=scalariformStyle.properties --quiet %s",
+ "match_files": [".*scala$"],
+ "print_filename": False,
+ "commit_changes": True,
+ },
+]
+
+
+def matches_file(file_name, match_files):
+ return any(re.compile(match_file).match(file_name) for match_file
+ in match_files)
+
+
+def check_files(files, check):
+ result = 0
+ print(check["output"])
+ for file_name in files:
+
+ if not "match_files" in check or \
+ matches_file(file_name, check["match_files"]):
+
+ if not "ignore_files" in check or \
+ not matches_file(file_name, check["ignore_files"]):
+
+ process = subprocess.Popen(check["command"] % file_name,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+ shell=True)
+
+ out, err = process.communicate()
+ if out or err:
+ if check["print_filename"]:
+ prefix = "\t%s:" % file_name
+ else:
+ prefix = "\t"
+ output_lines = ["%s%s" % (prefix, line) for
+ line in out.splitlines()]
+ print("\n".join(output_lines))
+ if err:
+ print(err)
+ result = 1
+ elif check["commit_changes"]:
+ p = subprocess.Popen(["git", "add", file_name],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ p.communicate()
+ return result
+
+
+def main(all_files):
+ # Check that the required linters and code checkers are all present
+ for check in CHECKS:
+ p = subprocess.Popen(["which", check["exe"]], stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ out, err = p.communicate()
+ if not out:
+ print("Required commit hook executable '%s' not found." % check["exe"])
+ sys.exit(1)
+
+ # Stash any changes to the working tree that are not going to be committed
+ subprocess.call(["git", "stash", "-u", "--keep-index"], stdout=subprocess.PIPE)
+
+ files = []
+ if all_files:
+ for root, dirs, file_names in os.walk("."):
+ for file_name in file_names:
+ files.append(os.path.join(root, file_name))
+ else:
+ p = subprocess.Popen(["git", "status", "--porcelain"],
+ stdout=subprocess.PIPE)
+ out, err = p.communicate()
+ for line in out.splitlines():
+ match = modified.match(line)
+ if match:
+ files.append(match.group("name"))
+
+ result = 0
+ for check in CHECKS:
+ result = check_files(files, check) or result
+
+ # Strategy:
+ # - Check if the linters made any changes
+ # - If there are no changes, pop the stash and commit
+ # - Otherwise:
+ # - Stash the change
+ # - Pop stash@{1}
+ # - Checkout stash@{0}
+ # - Drop stash@{0} (cannot pop directly since stash may conflict)
+ # - Commit
+ # This is because the initial stash will conflict with any possible
+ # changes made by the linters
+ p = subprocess.Popen(["git", "status", "--porcelain"],
+ stdout=subprocess.PIPE)
+ out, err = p.communicate()
+ if not out.strip():
+ subprocess.call(["git", "stash", "pop"],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ else:
+ subprocess.call(["git", "stash"],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ subprocess.call(["git", "stash", "pop", "--quiet", "--index", "stash@{1}"],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ subprocess.call(["git", "checkout", "stash", "--", "."],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ subprocess.call(["git", "stash", "drop"],
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ sys.exit(result)
+
+
+if __name__ == "__main__":
+
+ all_files = False
+
+ if len(sys.argv) > 1 and sys.argv[1] == "--all-files":
+ all_files = True
+
+ main(all_files)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index 17df80bf4cede5cc5c530a5ba83aa6dbcc668efd..2760ead8853b1cdd4c61a1906a13062bdb363045 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -19,6 +19,9 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
@Output(doc = "Output fastq file")
var fastq_output: File = _
+ @Output(doc = "Output statistics file")
+ var stats_output: File = _
+
executable = config("exe", default = "cutadapt")
override def versionCommand = executable + " --version"
override val versionRegex = """(.*)""".r
@@ -49,7 +52,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
optional("-M", opt_maximum_length) +
// input / output
required(fastq_input) +
- " > " + required(fastq_output)
+ required("--output", fastq_output) +
+ " > " + required(stats_output)
} else {
analysisName = getClass.getSimpleName + "-ln"
"ln -sf " +
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
index d31ce0ffbad4d582b1d37b663acc640aad187971..e29f8a5997cfe333f7bb9691613837ccf86aa564 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
@@ -11,25 +11,25 @@ import nl.lumc.sasc.biopet.core.config._
class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "R1 input")
- var input_R1: File = null
+ var input_R1: File = _
@Input(doc = "R2 input", required = false)
- var input_R2: File = null
+ var input_R2: File = _
@Input(doc = "qualityType file", required = false)
var qualityTypeFile: File = _
@Output(doc = "R1 output")
- var output_R1: File = null
+ var output_R1: File = _
@Output(doc = "R2 output", required = false)
- var output_R2: File = null
+ var output_R2: File = _
@Output(doc = "singles output", required = false)
- var output_singles: File = null
+ var output_singles: File = _
@Output(doc = "stats output")
- var output_stats: File = null
+ var output_stats: File = _
executable = config("exe", default = "sickle")
var qualityType: String = config("qualitytype")
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 00eb4cba9f707b308c25504e1578c02911cf4b7f..ecc911a7720341d2a8e9d4957adceb0875f72238 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -128,13 +128,19 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var R2: File = new File(R2_in)
if (!skipClip) { // Adapter clipping
+
val cutadapt_R1 = new Cutadapt(this)
+
if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
cutadapt_R1.fastq_input = R1
cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip" + R1_ext)
+ cutadapt_R1.stats_output = swapExt(outDir, R1, R1_ext, ".clip.stats")
+
if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
+
add(cutadapt_R1)
R1 = cutadapt_R1.fastq_output
+
if (paired) {
val cutadapt_R2 = new Cutadapt(this)
if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
diff --git a/scalariformStyle.properties b/scalariformStyle.properties
index 7e5f561df9c86dfbe0cc7608f49c6248027e0ba3..eb4298d0ee410be3bffedcc178bd4ecba1c94234 100644
--- a/scalariformStyle.properties
+++ b/scalariformStyle.properties
@@ -9,6 +9,7 @@ formatXml=true
indentLocalDefs=false
indentPackageBlocks=true
indentSpaces=2
+placeScaladocAsterisksBeneathSecondAsterisk=false
preserveDanglingCloseParenthesis=false
preserveSpaceBeforeArguments=false
rewriteArrowSymbols=false