From 8b27e8aa44e3c40e6d72126a4a802717c51dd7a0 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 8 Jun 2018 11:58:36 +0200
Subject: [PATCH] styling and paths
---
gatk.wdl | 132 ++++++++++++++++++++++++++---------------------------
picard.wdl | 22 ++++-----
2 files changed, 77 insertions(+), 77 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 12b03d9..37d6035 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -114,16 +114,16 @@ task GatherBqsrReports {
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
task HaplotypeCallerGvcf {
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
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
+ Array[File]+ intervalList
+ String gvcfPath
+ File refDict
+ File refFasta
+ File refFastaIndex
Float? contamination
- Int? compression_level
- String gatk_jar
+ Int? compressionLevel
+ String gatkJar
Float? memory
Float? memoryMultiplier
@@ -132,20 +132,20 @@ task HaplotypeCallerGvcf {
command {
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} \
HaplotypeCaller \
- -R ${ref_fasta} \
- -O ${gvcf_basename}.vcf.gz \
- -I ${sep=" -I " input_bams} \
- -L ${sep=' -L ' interval_list} \
+ -R ${refFasta} \
+ -O ${gvcfPath} \
+ -I ${sep=" -I " inputBams} \
+ -L ${sep=' -L ' intervalList} \
-contamination ${default=0 contamination} \
-ERC GVCF
}
output {
- File output_gvcf = "${gvcf_basename}.vcf.gz"
- File output_gvcf_index = "${gvcf_basename}.vcf.gz.tbi"
+ File outputGVCF = gvcfPath
+ File outputGVCFindex = gvcfPath + ".tbi"
}
runtime {
@@ -155,22 +155,22 @@ 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 +179,22 @@ 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{
@@ -204,19 +204,19 @@ task GenotypeGVCFs {
task CombineGVCFs {
String? preCommand
- Array[File]+ gvcf_files
- Array[File]+ gvcf_file_indexes
+ Array[File]+ gvcfFiles
+ Array[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
- Int? compression_level
+ Int? compressionLevel
Float? memory
Float? memoryMultiplier
@@ -225,23 +225,23 @@ task CombineGVCFs {
set -e -o pipefail
${preCommand}
- if [ ${length(gvcf_files)} -gt 1 ]; then
- java ${"-Dsamjdk.compression_level=" + compression_level} \
- -Xmx${mem}G -jar ${gatk_jar} \
+ if [ ${length(gvcfFiles)} -gt 1 ]; then
+ java ${"-Dsamjdk.compression_level=" + compressionLevel} \
+ -Xmx${mem}G -jar ${gatkJar} \
CombineGVCFs \
- -R ${ref_fasta} \
- -O ${output_basename + ".vcf.gz"} \
- -V ${sep=' -V ' gvcf_files} \
+ -R ${refFasta} \
+ -O ${outputPath} \
+ -V ${sep=' -V ' gvcfFiles} \
-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"}
+ ln -sf ${select_first(gvcfFiles)} ${outputPath}
+ ln -sf ${select_first(gvcfFileIndexes)} ${outputPath}.tbi
fi
}
output {
- File output_gvcf = output_basename + ".vcf.gz"
- File output_gvcf_index = output_basename + ".vcf.gz.tbi"
+ File outputGVCF = outputPath
+ File outputGVCFindex = outputPath + ".tbi"
}
runtime {
@@ -252,13 +252,13 @@ 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 +268,17 @@ 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 bam_index = sub(outputBam, "\\.bam$", ".bai")
}
runtime {
diff --git a/picard.wdl b/picard.wdl
index e3bcbc1..5f35122 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 {
--
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