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Commit 75742e19 authored by Cats's avatar Cats
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adjust memory

parent b0d40e66
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1 merge request!8Run time settings and additional adjustments
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biopet.wdl
+ 2
− 2
View file @ 75742e19
......@@ -65,7 +65,7 @@ task SampleConfig {
set -e -o pipefail
${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
java -Xmx${true=""+memory false="3" defined(memory)}G -jar ${tool_jar} \
java -Xmx${true=""+memory false="4" defined(memory)}G -jar ${tool_jar} \
-i ${sep="-i " inputFiles} \
${"--sample " + sample} \
${"--library " + library} \
......@@ -82,7 +82,7 @@ task SampleConfig {
}
runtime {
memory: ceil(select_first([memory, 3.0]) * select_first([memoryMultiplier, 2.0]))
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.0]))
}
}
......
gatk.wdl
+ 32
− 13
View file @ 75742e19
......@@ -33,7 +33,7 @@ task BaseRecalibrator {
}
runtime {
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2]))
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -50,10 +50,14 @@ task ApplyBQSR {
File ref_fasta_index
Int? compression_level
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java ${"-Dsamjdk.compression_level=" + compression_level} -Xms4G -jar ${gatk_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xms${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
......@@ -72,7 +76,7 @@ task ApplyBQSR {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -83,10 +87,13 @@ task GatherBqsrReports {
Array[File] input_bqsr_reports
String output_report_filepath
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java -Xms3G -jar ${gatk_jar} \
java -Xms${true=memory false="3" defined(memory)}G -jar ${gatk_jar} \
GatherBQSRReports \
-I ${sep=' -I ' input_bqsr_reports} \
-O ${output_report_filepath}
......@@ -97,7 +104,7 @@ task GatherBqsrReports {
}
runtime {
memory: 4
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -115,10 +122,14 @@ task HaplotypeCallerGvcf {
Int? compression_level
String gatk_jar
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${gatk_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
HaplotypeCaller \
-R ${ref_fasta} \
-O ${gvcf_basename}.vcf.gz \
......@@ -134,7 +145,7 @@ task HaplotypeCallerGvcf {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -156,12 +167,15 @@ task GenotypeGVCFs {
File dbsnp_vcf_index
Int? compression_level
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${gatk_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
GenotypeGVCFs \
-R ${ref_fasta} \
-O ${output_basename + ".vcf.gz"} \
......@@ -179,7 +193,7 @@ task GenotypeGVCFs {
}
runtime{
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -198,13 +212,16 @@ task CombineGVCFs {
File ref_dict
Int? compression_level
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
if [ ${length(gvcf_files)} -gt 1 ]; then
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${gatk_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
CombineGVCFs \
-R ${ref_fasta} \
-O ${output_basename + ".vcf.gz"} \
......@@ -222,7 +239,7 @@ task CombineGVCFs {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -237,11 +254,13 @@ task SplitNCigarReads {
String gatk_jar
Array[File]+ intervals
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java -Xms4G -jar ${gatk_jar} \
java -Xms${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
-I ${input_bam} \
-R ${ref_fasta} \
-O ${output_bam} # might have to be -o depending on GATK version \
......@@ -254,6 +273,6 @@ task SplitNCigarReads {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
htseq.wdl
+ 3
− 1
View file @ 75742e19
......@@ -7,6 +7,8 @@ task HTSeqCount {
String? order
String? stranded
Int? memory
command {
set -e -o pipefail
${preCommand}
......@@ -24,6 +26,6 @@ task HTSeqCount {
}
runtime {
memory: 3
memory: select_first([memory, 3])
}
}
\ No newline at end of file
picard.wdl
+ 23
− 8
View file @ 75742e19
......@@ -4,11 +4,14 @@ task ScatterIntervalList {
Int scatter_count
String picard_jar
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
mkdir scatter_list
java -Xmx4G -jar ${picard_jar} \
java -Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
IntervalListTools \
SCATTER_COUNT=${scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
......@@ -24,7 +27,7 @@ task ScatterIntervalList {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -36,10 +39,14 @@ task GatherBamFiles {
Int? compression_level
String picard_jar
Float? memory
Float? memoryMultiplier
command {
set -e -o pipefail
${preCommand}
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${picard_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
GatherBamFiles \
INPUT=${sep=' INPUT=' input_bams} \
OUTPUT=${output_bam_path} \
......@@ -54,7 +61,7 @@ task GatherBamFiles {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -67,6 +74,9 @@ task MarkDuplicates {
Int? compression_level
String picard_jar
Float? memory
Float? memoryMultiplier
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
# Sometimes we wish to supply "null" in order to turn off optical duplicate detection
# This can be desirable if you don't mind the estimated library size being wrong and optical duplicate detection is taking >7 days and failing
......@@ -79,7 +89,8 @@ task MarkDuplicates {
set -e -o pipefail
${preCommand}
mkdir -p $(dirname ${output_bam_path})
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${picard_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
MarkDuplicates \
INPUT=${sep=' INPUT=' input_bams} \
OUTPUT=${output_bam_path} \
......@@ -99,7 +110,7 @@ task MarkDuplicates {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
......@@ -112,12 +123,16 @@ task MergeVCFs {
Int? compression_level
String picard_jar
Float? memory
Float? memoryMultiplier
# Using MergeVcfs instead of GatherVcfs so we can create indices
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
command {
set -e -o pipefail
${preCommand}
java ${"-Dsamjdk.compression_level=" + compression_level} -Xmx4G -jar ${picard_jar} \
java ${"-Dsamjdk.compression_level=" + compression_level} \
-Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
MergeVcfs \
INPUT=${sep=' INPUT=' input_vcfs} \
OUTPUT=${output_vcf_path}
......@@ -129,6 +144,6 @@ task MergeVCFs {
}
runtime {
memory: 6
memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
}
}
\ No newline at end of file
star.wdl
+ 4
− 2
View file @ 75742e19
......@@ -13,6 +13,8 @@ task Star {
String? twopassMode
Array[String]? outSAMattrRGline
Float? memory
#TODO needs to be extended for all possible output extensions
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
......@@ -37,7 +39,7 @@ task Star {
}
runtime {
threads: select_first([runThreadN])
memory: 10
threads: select_first([runThreadN, 1])
memory: select_first([memory, 10])
}
}
\ No newline at end of file
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