diff --git a/biopet.wdl b/biopet.wdl
index 93dab22236fd00f9343d353c9048d1c1c6e21706..7d0d0a5fcfe5f1cb9711a3da6b3665f34546e3a8 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -1,3 +1,70 @@
+# PLEASE ADD TASKS IN ALPHABETIC ORDER.
+# This makes searching a lot easier.
+task BaseCounter {
+ String? preCommand
+ String tool_jar #Should this be of type File?
+ File bam
+ File refFlat
+ String outputDir
+ String prefix
+
+ Float? memory
+ Float? memoryMultiplier
+
+ Int mem = ceil(select_first([memory, 12.0]))
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ mkdir -p ${outputDir}
+ java -Xmx${mem}G -jar ${tool_jar} \
+ -b ${bam} \
+ -r ${refFlat} \
+ -o ${outputDir} \
+ -p ${prefix}
+ }
+
+ output {
+ File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
+ File exon = outputDir + "/" + prefix + ".base.exon.counts"
+ File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
+ File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
+ File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
+ File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
+ File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
+ File gene = outputDir + "/" + prefix + ".base.gene.counts"
+ File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
+ File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
+ File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
+ File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
+ File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
+ File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
+ File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
+ File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
+ File intron = outputDir + "/" + prefix + ".base.intron.counts"
+ File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
+ File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
+ File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
+ File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
+ File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
+ File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
+ File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
+ File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
+ File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
+ File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
+ File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
+ File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
+ File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
+ File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
+ File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
+ File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
+ File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+ }
+
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ }
+}
+
task FastqSplitter {
String? preCommand
File inputFastq
@@ -23,36 +90,30 @@ task FastqSplitter {
}
}
-task ScatterRegions {
+task FastqSync {
String? preCommand
- File ref_fasta
- File ref_dict
- String outputDirPath
- String tool_jar
- Int? scatterSize
- File? regions
-
- Float? memory
- Float? memoryMultiplier
-
- Int mem = ceil(select_first([memory, 4.0]))
+ File ref1
+ File ref2
+ File in1
+ File in2
+ String out1path
+ String out2path
+ File tool_jar
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${outputDirPath}
- java -Xmx${mem}G -jar ${tool_jar} \
- -R ${ref_fasta} \
- -o ${outputDirPath} \
- ${"-s " + scatterSize} \
- ${"-L " + regions}
+ mkdir -p $(dirname ${out1path}) $(dirname ${out2path})
+ java -jar ${tool_jar} \
+ --in1 ${in1} \
+ --in2 ${in2} \
+ --ref1 ${ref1} \
+ --ref2 ${ref2} \
+ --out1 ${out1path} \
+ --out2 ${out2path}
}
-
output {
- Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
- }
-
- runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ File out1 = out1path
+ File out2 = out2path
}
}
@@ -94,67 +155,36 @@ task SampleConfig {
}
}
-task BaseCounter {
+task ScatterRegions {
String? preCommand
- String tool_jar #Should this be of type File?
- File bam
- File refFlat
- String outputDir
- String prefix
+ File ref_fasta
+ File ref_dict
+ String outputDirPath
+ String tool_jar
+ Int? scatterSize
+ File? regions
Float? memory
Float? memoryMultiplier
- Int mem = ceil(select_first([memory, 12.0]))
+ Int mem = ceil(select_first([memory, 4.0]))
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${outputDir}
+ mkdir -p ${outputDirPath}
java -Xmx${mem}G -jar ${tool_jar} \
- -b ${bam} \
- -r ${refFlat} \
- -o ${outputDir} \
- -p ${prefix}
+ -R ${ref_fasta} \
+ -o ${outputDirPath} \
+ ${"-s " + scatterSize} \
+ ${"-L " + regions}
}
output {
- File exonAntisense = outputDir + "/" + prefix + ".base.exon.antisense.counts"
- File exon = outputDir + "/" + prefix + ".base.exon.counts"
- File exonMergeAntisense = outputDir + "/" + prefix + ".base.exon.merge.antisense.counts"
- File exonMerge = outputDir + "/" + prefix + ".base.exon.merge.counts"
- File exonMergeSense = outputDir + "/" + prefix + ".base.exon.merge.sense.counts"
- File exonSense = outputDir + "/" + prefix + ".base.exon.sense.counts"
- File geneAntisense = outputDir + "/" + prefix + ".base.gene.antisense.counts"
- File gene = outputDir + "/" + prefix + ".base.gene.counts"
- File geneExonicAntisense = outputDir + "/" + prefix + ".base.gene.exonic.antisense.counts"
- File geneExonic = outputDir + "/" + prefix + ".base.gene.exonic.counts"
- File geneExonicSense = outputDir + "/" + prefix + ".base.gene.exonic.sense.counts"
- File geneIntronicAntisense = outputDir + "/" + prefix + ".base.gene.intronic.antisense.counts"
- File geneIntronic = outputDir + "/" + prefix + ".base.gene.intronic.counts"
- File geneIntronicSense = outputDir + "/" + prefix + ".base.gene.intronic.sense.counts"
- File geneSense = outputDir + "/" + prefix + ".base.gene.sense.counts"
- File intronAntisense = outputDir + "/" + prefix + ".base.intron.antisense.counts"
- File intron = outputDir + "/" + prefix + ".base.intron.counts"
- File intronMergeAntisense = outputDir + "/" + prefix + ".base.intron.merge.antisense.counts"
- File intronMerge = outputDir + "/" + prefix + ".base.intron.merge.counts"
- File intronMergeSense = outputDir + "/" + prefix + ".base.intron.merge.sense.counts"
- File intronSense = outputDir + "/" + prefix + ".base.intron.sense.counts"
- File metaExonsNonStranded = outputDir + "/" + prefix + ".base.metaexons.non_stranded.counts"
- File metaExonsStrandedAntisense = outputDir + "/" + prefix + ".base.metaexons.stranded.antisense.counts"
- File metaExonsStranded = outputDir + "/" + prefix + ".base.metaexons.stranded.counts"
- File metaExonsStrandedSense = outputDir + "/" + prefix + ".base.metaexons.stranded.sense.counts"
- File transcriptAntisense = outputDir + "/" + prefix + ".base.transcript.antisense.counts"
- File transcript = outputDir + "/" + prefix + ".base.transcript.counts"
- File transcriptExonicAntisense = outputDir + "/" + prefix + ".base.transcript.exonic.antisense.counts"
- File transcriptExonic = outputDir + "/" + prefix + ".base.transcript.exonic.counts"
- File transcriptExonicSense = outputDir + "/" + prefix + ".base.transcript.exonic.sense.counts"
- File transcriptIntronicAntisense = outputDir + "/" + prefix + ".base.transcript.intronic.antisense.counts"
- File transcriptIntronic = outputDir + "/" + prefix + ".base.transcript.intronic.counts"
- File transcriptIntronicSense = outputDir + "/" + prefix + ".base.transcript.intronic.sense.counts"
- File transcriptSense = outputDir + "/" + prefix + ".base.transcript.sense.counts"
+ Array[File] scatters = glob(outputDirPath + "/scatter-*.bed")
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
}
}
+
diff --git a/bwa.wdl b/bwa.wdl
index ffa42313dad13f0c13df6f9c77f938567c0027a0..440b6559b2fcceaa0efaebfdeddd35b46da07d5a 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -1,8 +1,8 @@
-task BwaMem {
+task mem {
String? preCommand
File inputR1
File? inputR2
- String referenceFasta
+ File referenceFasta
Array[File] indexFiles # These indexFiles need to be added, otherwise cromwell will not find them.
String outputPath
String? readgroup
@@ -10,6 +10,7 @@ task BwaMem {
Int? threads
Int? memory
+
command {
set -e -o pipefail
mkdir -p $(dirname ${outputPath})
@@ -23,8 +24,8 @@ task BwaMem {
File bamFile = outputPath
}
runtime{
- cpu: if defined(threads) then threads else 1
- memory: if defined(memory) then memory else 8
+ cpu: select_first([threads,1])
+ memory: select_first([memory,8])
}
}
@@ -35,6 +36,7 @@ task index {
Int? blockSize
String? outputDir
String fastaFilename = basename(fasta)
+ String outputFile = if (defined(outputDir)) then outputDir + "/" + fastaFilename else fasta
command {
set -e -o pipefail
@@ -47,13 +49,12 @@ task index {
bwa index \
${"-a " + constructionAlgorithm} \
${"-b" + blockSize} \
- ${outputDir + "/"}${fastaFilename}
+ ${outputFile}
}
output {
- File indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
- File indexedFasta = indexBase
- Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
+ File indexedFasta = outputFile
+ Array[File] indexFiles = [outputFile + ".bwt",outputFile + ".pac",outputFile + ".sa",outputFile + ".amb",outputFile + ".ann"]
}
parameter_meta {
fasta: "Fasta file to be indexed"
diff --git a/picard.wdl b/picard.wdl
index 104261816f42dea6126dc5c645ab7871e618fe1e..2c638df3bc4ae1d98261393d2f74012c692eb3e0 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -147,6 +147,41 @@ task MergeVCFs {
File output_vcf_index = output_vcf_path + ".tbi"
}
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
+ }
+}
+
+task SamToFastq {
+ String? preCommand
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputUnpaired
+ String picard_jar
+ Float? memory
+ Float? memoryMultiplier
+ Int mem = ceil(select_first([memory, 16.0])) # High memory default to avoid crashes.
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ java \
+ -Xmx${mem}G \
+ -jar ${picard_jar} \
+ SamToFastq \
+ I=${inputBam} \
+ ${"FASTQ=" + outputRead1} \
+ ${"SECOND_END_FASTQ=" + outputRead2} \
+ ${"UNPAIRED_FASTQ=" + outputUnpaired}
+ }
+
+ output {
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? unpairedRead = outputUnpaired
+ }
+
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 1.5]))
}
diff --git a/samtools.wdl b/samtools.wdl
index a1192ac3a08419a8584c01a005cd785649a7d60d..59f5b0eadb9575becb1d783c6e2ddec310fbee68 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -117,3 +117,40 @@ task fastq {
}
}
+
+task view {
+ String? preCommand
+ File inFile
+ File? referenceFasta
+ String outputFileName
+ Boolean? outputBam
+ Boolean? uncompressedBamOutput
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Int? threads
+ Int? memory
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ samtools view \
+ ${"-T " + referenceFasta} \
+ ${"-o " + outputFileName} \
+ ${true="-b " false="" outputBam} \
+ ${true="-u " false="" uncompressedBamOutput} \
+ ${"-f " + includeFilter} \
+ ${"-F " + excludeFilter} \
+ ${"-G " + excludeSpecificFilter} \
+ ${"--threads " + threads - 1} \
+ ${inFile}
+ }
+
+ output {
+ File outputFile = outputFileName
+ }
+ runtime {
+ cpu: select_first([threads, 1])
+ memory: select_first([memory, 1])
+ }
+}
diff --git a/spades.wdl b/spades.wdl
index ce9de29cecb0b48d20faff177fc1a007e0e7c312..f0feb573ec4fb71f09ec5cb42f62fe45c4ed7cb8 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -22,14 +22,15 @@ task spades {
Boolean? disableRepeatResolution
File? dataset
Int? threads
- Int? memoryGb
+ Float? memoryGb
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
Int finalThreads = select_first([threads,1])
- Int totalMemory = select_first([memoryGb, finalThreads * 16])
- Int clusterMemory = totalMemory / finalThreads
+ Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
+ Int finalMemory = ceil(totalMemory)
+ Int clusterMemory = ceil(totalMemory / finalThreads)
command {
set -e -o pipefail
@@ -57,7 +58,7 @@ task spades {
${true="--disable-rr" false="" disableRepeatResolution } \
${"--dataset " + dataset } \
${"--threads " + finalThreads} \
- ${"--memory " + totalMemory } \
+ ${"--memory " + finalMemory } \
${"-k " + k } \
${"--cov-cutoff " + covCutoff } \
${"--phred-offset " + phredOffset }