diff --git a/biopet.wdl b/biopet.wdl
index ea8d2ba4233d8a1373c701c33b3b052388d825dc..b3234e4d16543afcbdc8bce39616010ce5463fde 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -117,25 +117,24 @@ task extractAdaptersFastqc {
task FastqSplitter {
String? preCommand
File inputFastq
- String outputPath
- Int numberChunks
- File toolJar
- Array[Int] chunks = range(numberChunks)
+ Array[String] outputPaths
+ String toolJar
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
- if [ ${numberChunks} -gt 1 ]; then
- SEP="/${basename(inputFastq)} -o "
- java -jar ${toolJar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
- else
- ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
- fi
+ mkdir -p $(dirname ${sep=') $(dirname ' outputPaths})
+ if [ ${length(outputPaths)} -gt 1 ]; then
+ java -jar ${toolJar} \
+ -I ${inputFastq} \
+ -o ${sep=' -o ' outputPaths}
+ else
+ ln -sf ${inputFastq} ${outputPaths[0]}
+ fi
}
output {
- Array[File] outputFastqFiles = glob(outputPath + "/chunk_*/" + basename(inputFastq))
+ Array[File] chunks = outputPaths
}
}
diff --git a/common.wdl b/common.wdl
index 2ac9cb99366ab27e768c29a947bf239064193186..d80d47e6d5a964b4ba2637741eeb62b51cecc2f2 100644
--- a/common.wdl
+++ b/common.wdl
@@ -106,7 +106,9 @@ task appendToStringArray {
}
task createLink {
- File inputFile
+ # Making this of type File will create a link to the copy of the file in the execution
+ # folder, instead of the actual file.
+ String inputFile
String outputPath
command {
diff --git a/gatk.wdl b/gatk.wdl
index 12b03d9820f79aa8cc420e073b8a36a355ddaa71..b5fd4a8d78ab641fd99abf6da0ae1a26f4212c7f 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1,16 +1,16 @@
-# Generate Base Quality Score Recalibration (BQSR) model
-task BaseRecalibrator {
+# Apply Base Quality Score Recalibration (BQSR) model
+task ApplyBQSR {
String? preCommand
- String gatk_jar
- String input_bam
- String input_bam_index
- String recalibration_report_filename
- Array[File]+ sequence_group_interval
- Array[File]+ known_indels_sites_VCFs
- Array[File]+ known_indels_sites_indices
- File ref_dict
- File ref_fasta
- File ref_fasta_index
+ File gatkJar
+ File inputBam
+ File inputBamIndex
+ String outputBamPath
+ File recalibrationReport
+ Array[File]+ sequenceGroupInterval
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -19,18 +19,23 @@ task BaseRecalibrator {
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatk_jar} \
- BaseRecalibrator \
- -R ${ref_fasta} \
- -I ${input_bam} \
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xms${mem}G -jar ${gatkJar} \
+ ApplyBQSR \
+ --create-output-bam-md5 \
+ --add-output-sam-program-record \
+ -R ${refFasta} \
+ -I ${inputBam} \
--use-original-qualities \
- -O ${recalibration_report_filename} \
- --known-sites ${sep=" --known-sites " known_indels_sites_VCFs} \
- -L ${sep=" -L " sequence_group_interval}
+ -O ${outputBamPath} \
+ -bqsr ${recalibrationReport} \
+ --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
+ -L ${sep=" -L " sequenceGroupInterval}
}
output {
- File recalibration_report = "${recalibration_report_filename}"
+ File recalibrated_bam = outputBamPath
+ File recalibrated_bam_checksum = outputBamPath + ".md5"
}
runtime {
@@ -38,18 +43,19 @@ task BaseRecalibrator {
}
}
-# Apply Base Quality Score Recalibration (BQSR) model
-task ApplyBQSR {
+# Generate Base Quality Score Recalibration (BQSR) model
+task BaseRecalibrator {
String? preCommand
- String gatk_jar
- String input_bam
- String output_bam_path
- File recalibration_report
- Array[String] sequence_group_interval
- File ref_dict
- File ref_fasta
- File ref_fasta_index
- Int? compression_level
+ File gatkJar
+ File inputBam
+ File inputBamIndex
+ String recalibrationReportPath
+ Array[File]+ sequenceGroupInterval
+ Array[File]+ knownIndelsSitesVCFs
+ Array[File]+ knownIndelsSitesIndices
+ File refDict
+ File refFasta
+ File refFastaIndex
Float? memory
Float? memoryMultiplier
@@ -58,23 +64,18 @@ task ApplyBQSR {
command {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xms${mem}G -jar ${gatk_jar} \
- ApplyBQSR \
- --create-output-bam-md5 \
- --add-output-sam-program-record \
- -R ${ref_fasta} \
- -I ${input_bam} \
+ java -Xms${mem}G -jar ${gatkJar} \
+ BaseRecalibrator \
+ -R ${refFasta} \
+ -I ${inputBam} \
--use-original-qualities \
- -O ${output_bam_path} \
- -bqsr ${recalibration_report} \
- --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
- -L ${sep=" -L " sequence_group_interval}
+ -O ${recalibrationReportPath} \
+ --known-sites ${sep=" --known-sites " knownIndelsSitesVCFs} \
+ -L ${sep=" -L " sequenceGroupInterval}
}
output {
- File recalibrated_bam = "${output_bam_path}"
- File recalibrated_bam_checksum = "${output_bam_path}.md5"
+ File recalibrationReport = recalibrationReportPath
}
runtime {
@@ -82,13 +83,21 @@ task ApplyBQSR {
}
}
-# Combine multiple recalibration tables from scattered BaseRecalibrator runs
-task GatherBqsrReports {
+task CombineGVCFs {
String? preCommand
- String gatk_jar
- Array[File] input_bqsr_reports
- String output_report_filepath
+ Array[File]+ gvcfFiles
+ Array[File]+ gvcfFileIndexes
+ Array[File]+ intervals
+
+ String outputPath
+
+ String gatkJar
+ File refFasta
+ File refFastaIndex
+ File refDict
+
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -96,14 +105,24 @@ task GatherBqsrReports {
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatk_jar} \
- GatherBQSRReports \
- -I ${sep=' -I ' input_bqsr_reports} \
- -O ${output_report_filepath}
+
+ if [ ${length(gvcfFiles)} -gt 1 ]; then
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
+ CombineGVCFs \
+ -R ${refFasta} \
+ -O ${outputPath} \
+ -V ${sep=' -V ' gvcfFiles} \
+ -L ${sep=' -L ' intervals}
+ else # TODO this should be handeled in wdl
+ ln -sf ${select_first(gvcfFiles)} ${outputPath}
+ ln -sf ${select_first(gvcfFileIndexes)} ${outputPath}.tbi
+ fi
}
output {
- File output_bqsr_report = "${output_report_filepath}"
+ File outputGVCF = outputPath
+ File outputGVCFindex = outputPath + ".tbi"
}
runtime {
@@ -111,19 +130,12 @@ task GatherBqsrReports {
}
}
-# Call variants on a single sample with HaplotypeCaller to produce a GVCF
-task HaplotypeCallerGvcf {
+# Combine multiple recalibration tables from scattered BaseRecalibrator runs
+task GatherBqsrReports {
String? preCommand
- Array[File]+ input_bams
- Array[File]+ input_bams_index
- Array[File]+ interval_list
- String gvcf_basename
- File ref_dict
- File ref_fasta
- File ref_fasta_index
- Float? contamination
- Int? compression_level
- String gatk_jar
+ String gatkJar
+ Array[File] inputBQSRreports
+ String outputReportPath
Float? memory
Float? memoryMultiplier
@@ -132,20 +144,14 @@ task HaplotypeCallerGvcf {
command {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${mem}G -jar ${gatk_jar} \
- HaplotypeCaller \
- -R ${ref_fasta} \
- -O ${gvcf_basename}.vcf.gz \
- -I ${sep=" -I " input_bams} \
- -L ${sep=' -L ' interval_list} \
- -contamination ${default=0 contamination} \
- -ERC GVCF
+ java -Xms${mem}G -jar ${gatkJar} \
+ GatherBQSRReports \
+ -I ${sep=' -I ' inputBQSRreports} \
+ -O ${outputReportPath}
}
output {
- File output_gvcf = "${gvcf_basename}.vcf.gz"
- File output_gvcf_index = "${gvcf_basename}.vcf.gz.tbi"
+ File outputBQSRreport = outputReportPath
}
runtime {
@@ -155,22 +161,22 @@ task HaplotypeCallerGvcf {
task GenotypeGVCFs {
String? preCommand
- File gvcf_files
- File gvcf_file_indexes
+ File gvcfFiles
+ File gvcfFileIndexes
Array[File]+ intervals
- String output_basename
+ String outputPath
- String gatk_jar
+ String gatkJar
- File ref_fasta
- File ref_fasta_index
- File ref_dict
+ File refFasta
+ File refFastaIndex
+ File refDict
- File dbsnp_vcf
- File dbsnp_vcf_index
+ File dbsnpVCF
+ File dbsnpVCFindex
- Int? compression_level
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -179,22 +185,22 @@ task GenotypeGVCFs {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${mem}G -jar ${gatk_jar} \
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
GenotypeGVCFs \
- -R ${ref_fasta} \
- -O ${output_basename + ".vcf.gz"} \
- -D ${dbsnp_vcf} \
+ -R ${refFasta} \
+ -O ${outputPath} \
+ -D ${dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
- -V ${gvcf_files} \
+ -V ${gvcfFiles} \
-L ${sep=' -L ' intervals}
}
output {
- File output_vcf = output_basename + ".vcf.gz"
- File output_vcf_index = output_basename + ".vcf.gz.tbi"
+ File outputVCF = outputPath
+ File outputVCFindex = outputPath + ".tbi"
}
runtime{
@@ -202,21 +208,20 @@ task GenotypeGVCFs {
}
}
-task CombineGVCFs {
+# Call variants on a single sample with HaplotypeCaller to produce a GVCF
+task HaplotypeCallerGvcf {
String? preCommand
- Array[File]+ gvcf_files
- Array[File]+ gvcf_file_indexes
- Array[File]+ intervals
-
- String output_basename
-
- String gatk_jar
-
- File ref_fasta
- File ref_fasta_index
- File ref_dict
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
+ Array[File]+ intervalList
+ String gvcfPath
+ File refDict
+ File refFasta
+ File refFastaIndex
+ Float? contamination
+ Int? compressionLevel
+ String gatkJar
- Int? compression_level
Float? memory
Float? memoryMultiplier
@@ -224,24 +229,20 @@ task CombineGVCFs {
command {
set -e -o pipefail
${preCommand}
-
- if [ ${length(gvcf_files)} -gt 1 ]; then
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${mem}G -jar ${gatk_jar} \
- CombineGVCFs \
- -R ${ref_fasta} \
- -O ${output_basename + ".vcf.gz"} \
- -V ${sep=' -V ' gvcf_files} \
- -L ${sep=' -L ' intervals}
- else
- ln -sf ${select_first(gvcf_files)} ${output_basename + ".vcf.gz"}
- ln -sf ${select_first(gvcf_files)}.tbi ${output_basename + ".vcf.gz.tbi"}
- fi
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
+ HaplotypeCaller \
+ -R ${refFasta} \
+ -O ${gvcfPath} \
+ -I ${sep=" -I " inputBams} \
+ -L ${sep=' -L ' intervalList} \
+ -contamination ${default=0 contamination} \
+ -ERC GVCF
}
output {
- File output_gvcf = output_basename + ".vcf.gz"
- File output_gvcf_index = output_basename + ".vcf.gz.tbi"
+ File outputGVCF = gvcfPath
+ File outputGVCFindex = gvcfPath + ".tbi"
}
runtime {
@@ -252,13 +253,13 @@ task CombineGVCFs {
task SplitNCigarReads {
String? preCommand
- File input_bam
- File input_bam_index
- File ref_fasta
- File ref_fasta_index
- File ref_dict
- String output_bam
- String gatk_jar
+ File inputBam
+ File inputBamIndex
+ File refFasta
+ File refFastaIndex
+ File refDict
+ String outputBam
+ String gatkJar
Array[File]+ intervals
Float? memory
@@ -268,17 +269,17 @@ task SplitNCigarReads {
command {
set -e -o pipefail
${preCommand}
- java -Xms${mem}G -jar ${gatk_jar} \
+ java -Xms${mem}G -jar ${gatkJar} \
SplitNCigarReads \
- -I ${input_bam} \
- -R ${ref_fasta} \
- -O ${output_bam} \
+ -I ${inputBam} \
+ -R ${refFasta} \
+ -O ${outputBam} \
-L ${sep=' -L ' intervals}
}
output {
- File bam = output_bam
- File bam_index = sub(output_bam, "\\.bam$", ".bai")
+ File bam = outputBam
+ File bamIndex = sub(outputBam, "\\.bam$", ".bai")
}
runtime {
diff --git a/picard.wdl b/picard.wdl
index e3bcbc1320c1ef0ce4256f7bcd19400da3273235..5f35122130ede6f6ec93aeb84f060f3f982f6264 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -120,11 +120,11 @@ task MarkDuplicates {
# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
task MergeVCFs {
String? preCommand
- Array[File] input_vcfs
- Array[File] input_vcfs_indexes
- String output_vcf_path
- Int? compression_level
- String picard_jar
+ Array[File] inputVCFs
+ Array[File] inputVCFsIndexes
+ String outputVCFpath
+ Int? compressionLevel
+ String picardJar
Float? memory
Float? memoryMultiplier
@@ -135,16 +135,16 @@ task MergeVCFs {
command {
set -e -o pipefail
${preCommand}
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${mem}G -jar ${picard_jar} \
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${picardJar} \
MergeVcfs \
- INPUT=${sep=' INPUT=' input_vcfs} \
- OUTPUT=${output_vcf_path}
+ INPUT=${sep=' INPUT=' inputVCFs} \
+ OUTPUT=${outputVCFpath}
}
output {
- File output_vcf = output_vcf_path
- File output_vcf_index = output_vcf_path + ".tbi"
+ File outputVCF = outputVCFpath
+ File outputVCFindex = outputVCFpath + ".tbi"
}
runtime {