diff --git a/biopet.wdl b/biopet/biopet.wdl
similarity index 81%
rename from biopet.wdl
rename to biopet/biopet.wdl
index feb963fc2745f7d523025a3258a4a9f27a0280f7..9304f6f71b0cc2209dd46d4dcc5a30a678112381 100644
--- a/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -1,11 +1,12 @@
version 1.0
+import "common.wdl"
+
task BaseCounter {
input {
String? preCommand
File? toolJar
- File bam
- File bamIndex
+ IndexedBamFile bam
File refFlat
String outputDir
String prefix
@@ -23,7 +24,7 @@ task BaseCounter {
mkdir -p ~{outputDir}
~{preCommand}
~{toolCommand} \
- -b ~{bam} \
+ -b ~{bam.file} \
-r ~{refFlat} \
-o ~{outputDir} \
-p ~{prefix}
@@ -160,10 +161,8 @@ task FastqSplitter {
task FastqSync {
input {
String? preCommand
- File ref1
- File ref2
- File in1
- File in2
+ FastqPair refFastq
+ FastqPair inputFastq
String out1path
String out2path
File? toolJar
@@ -181,17 +180,19 @@ task FastqSync {
~{preCommand}
mkdir -p $(dirname ~{out1path}) $(dirname ~{out2path})
~{toolCommand} \
- --in1 ~{in1} \
- --in2 ~{in2} \
- --ref1 ~{ref1} \
- --ref2 ~{ref2} \
+ --in1 ~{inputFastq.R1} \
+ --in2 ~{inputFastq.R2} \
+ --ref1 ~{refFastq.R1} \
+ --ref2 ~{refFastq.R2} \
--out1 ~{out1path} \
--out2 ~{out2path}
}
output {
- File out1 = out1path
- File out2 = out2path
+ FastqPair out1 = object {
+ R1: out1path,
+ R1: out2path
+ }
}
runtime {
@@ -199,89 +200,10 @@ task FastqSync {
}
}
-task SampleConfig {
- input {
- File? toolJar
- String? preCommand
- Array[File]+ inputFiles
- String keyFilePath
- String? sample
- String? library
- String? readgroup
- String? jsonOutputPath
- String? tsvOutputPath
-
- Int memory = 4
- Float memoryMultiplier = 2.0
- }
-
- String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " +toolJar
- else "biopet-sampleconfig -Xmx" + memory + "G"
-
- command {
- set -e -o pipefail
- ~{preCommand}
- mkdir -p . ~{"$(dirname " + jsonOutputPath + ")"} ~{"$(dirname " + tsvOutputPath + ")"}
- ~{toolCommand} \
- -i ~{sep="-i " inputFiles} \
- ~{"--sample " + sample} \
- ~{"--library " + library} \
- ~{"--readgroup " + readgroup} \
- ~{"--jsonOutput " + jsonOutputPath} \
- ~{"--tsvOutput " + tsvOutputPath} \
- > ~{keyFilePath}
- }
-
- output {
- File keysFile = keyFilePath
- File? jsonOutput = jsonOutputPath
- File? tsvOutput = tsvOutputPath
- }
-
- runtime {
- memory: ceil(memory * memoryMultiplier)
- }
-}
-
-task SampleConfigCromwellArrays {
- input {
- File? toolJar
- String? preCommand
- Array[File]+ inputFiles
- String outputPath
-
- Int memory = 4
- Float memoryMultiplier = 2.0
- }
-
- String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-sampleconfig -Xmx" + memory + "G"
-
- command {
- set -e -o pipefail
- ~{preCommand}
- mkdir -p $(dirname ~{outputPath})
- ~{toolCommand} CromwellArrays \
- -i ~{sep="-i " inputFiles} \
- ~{"-o " + outputPath}
- }
-
- output {
- File outputFile = outputPath
- }
-
- runtime {
- memory: ceil(memory * memoryMultiplier)
- }
-}
-
task ScatterRegions {
input {
String? preCommand
- File refFasta
- File refDict
+ Reference reference
String outputDirPath
File? toolJar
Int? scatterSize
@@ -300,7 +222,7 @@ task ScatterRegions {
~{preCommand}
mkdir -p ~{outputDirPath}
~{toolCommand} \
- -R ~{refFasta} \
+ -R ~{reference.fasta} \
-o ~{outputDirPath} \
~{"-s " + scatterSize} \
~{"-L " + regions}
@@ -315,48 +237,13 @@ task ScatterRegions {
}
}
-task Seqstat {
- input {
- String? preCommand
- File? toolJar
- File fastq
- String outputFile
-
- Int memory = 4
- Float memoryMultiplier = 2.0
- }
-
- String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-seqstat -Xmx" + memory + "G"
-
- command {
- set -e -o pipefail
- ~{preCommand}
- mkdir -p $(dirname ~{outputFile})
- ~{toolCommand} \
- --fastq ~{fastq} \
- --output ~{outputFile}
- }
-
- output {
- File json = outputFile
- }
-
- runtime {
- memory: ceil(memory * memoryMultiplier)
- }
-}
-
task ValidateAnnotation {
input {
String? preCommand
File? toolJar
File? refRefflat
File? gtfFile
- File refFasta
- File refFastaIndex
- File refDict
+ Reference reference
Int memory = 4
Float memoryMultiplier = 2.0
@@ -372,7 +259,7 @@ task ValidateAnnotation {
~{toolCommand} \
~{"-r " + refRefflat} \
~{"-g " + gtfFile} \
- -R ~{refFasta}
+ -R ~{reference.fasta}
}
output {
@@ -388,8 +275,7 @@ task ValidateFastq {
input {
String? preCommand
File? toolJar
- File fastq1
- File? fastq2
+ FastqPair inputFastq
Int memory = 4
Float memoryMultiplier = 2.0
@@ -403,14 +289,13 @@ task ValidateFastq {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
- --fastq1 ~{fastq1} \
- ~{"--fastq2 " + fastq2}
+ --fastq1 ~{inputFastq.R1} \
+ ~{"--fastq2 " + inputFastq.R2}
}
output {
File stderr = stderr()
- File validatedFastq1 = fastq1
- File? validatedFastq2 = fastq2
+ FastqPair validatedFastq = inputFastq
}
runtime {
@@ -422,11 +307,8 @@ task ValidateVcf {
input {
String? preCommand
File? toolJar
- File vcfFile
- File vcfIndex
- File refFasta
- File refFastaIndex
- File refDict
+ IndexedVcfFile vcf
+ Reference reference
Int memory = 4
Float memoryMultiplier = 2.0
@@ -440,8 +322,8 @@ task ValidateVcf {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
- -i ~{vcfFile} \
- -R ~{refFasta}
+ -i ~{vcf.file} \
+ -R ~{reference.fasta}
}
output {
@@ -455,11 +337,8 @@ task ValidateVcf {
task VcfStats {
input {
- File vcfFile
- File vcfIndex
- File refFasta
- File refFastaIndex
- File refDict
+ IndexedVcfFile vcf
+ Reference reference
String outputDir
File? intervals
Array[String]+? infoTags
@@ -493,8 +372,8 @@ task VcfStats {
mkdir -p ~{outputDir}
~{preCommand}
~{toolCommand} \
- -I ~{vcfFile} \
- -R ~{refFasta} \
+ -I ~{vcf.file} \
+ -R ~{reference.fasta} \
-o ~{outputDir} \
-t ~{localThreads} \
~{"--intervals " + intervals} \
diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..d7ae6d274b19f312f4ccf04927e5a6e1c77f6b33
--- /dev/null
+++ b/biopet/sampleconfig.wdl
@@ -0,0 +1,77 @@
+task SampleConfig {
+ input {
+ File? toolJar
+ String? preCommand
+ Array[File]+ inputFiles
+ String keyFilePath
+ String? sample
+ String? library
+ String? readgroup
+ String? jsonOutputPath
+ String? tsvOutputPath
+
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-sampleconfig -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ mkdir -p . ~{"$(dirname " + jsonOutputPath + ")"} ~{"$(dirname " + tsvOutputPath + ")"}
+ ~{toolCommand} \
+ -i ~{sep="-i " inputFiles} \
+ ~{"--sample " + sample} \
+ ~{"--library " + library} \
+ ~{"--readgroup " + readgroup} \
+ ~{"--jsonOutput " + jsonOutputPath} \
+ ~{"--tsvOutput " + tsvOutputPath} \
+ > ~{keyFilePath}
+ }
+
+ output {
+ File keysFile = keyFilePath
+ File? jsonOutput = jsonOutputPath
+ File? tsvOutput = tsvOutputPath
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
+task SampleConfigCromwellArrays {
+ input {
+ File? toolJar
+ String? preCommand
+ Array[File]+ inputFiles
+ String outputPath
+
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-sampleconfig -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ mkdir -p $(dirname ~{outputPath})
+ ~{toolCommand} CromwellArrays \
+ -i ~{sep="-i " inputFiles} \
+ ~{"-o " + outputPath}
+ }
+
+ output {
+ File outputFile = outputPath
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}