diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33f85337a40d19520b36117a57720916ddbd3288..ccd1cedc6bb1cacff5002a792f74b17838583b23 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,8 +9,25 @@ This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
-version 3.2.0-develop
+version 4.0.0-develop
---------------------------
++ Added a log output for STAR.
++ Added report output to Hisat2.
++ Change MultiQC inputs. It now accepts an array of reports files. It does not
+ need access to a folder with the reports anymore. MultiQC can now be used
+ as a normal WDL task without hacks.
++ Picard: Make all outputs in `CollectMultipleMetrics` optional. This will make sure the
+ task will not fail if one of the metrics is set to false.
++ The struct `BowtieIndex` was removed, as it has become obsolete.
++ The task `ReorderGlobbedScatters` was removed, as it has become obsolete.
++ Adjusted the memory settings of many tools, especially java tools.
+ They should now more accurately represent actual memory usage (as
+ opposed to virtual memory).
++ Added `-XX:ParallelGCThreads=1` to the java options of java tasks.
++ Added `timeMinutes` input to many tasks, this indicates a maximum
+ number of minutes that the job will run. The associated runtime
+ attribute is `time_minutes` which can be used to inform
+ a scheduler (eg. slurm) of the run time of the job.
+ Added STAR GenomeGenerate task.
+ GATK.HaplotypeCaller: Add `--dont-use-soft-clipped-bases` and
`--standard-min-confidence-threshold-for-calling` options. These are
diff --git a/CPAT.wdl b/CPAT.wdl
index 098d9ca61cc84de480f0a407868541937def3650..3b542e4fcb2e88859d4723f25c4659f92eb277cb 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -31,6 +31,7 @@ task CPAT {
# CPAT should not index the reference genome.
Array[String]? startCodons
Array[String]? stopCodons
+ Int timeMinutes = 10 + ceil(size(gene, "G") * 30)
String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
}
@@ -55,6 +56,7 @@ task CPAT {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -67,6 +69,7 @@ task CPAT {
category: "advanced"}
startCodons: {description: "Equivalent to CPAT's `--start` option.", category: "advanced"}
stopCodons: {description: "Equivalent to CPAT's `--stop` option.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/bcftools.wdl b/bcftools.wdl
index 122fcdd1e4ee0a5cc468b9b1f15d884813ac5058..53165c6be2118579bc1705a11577b52e80c8591e 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -26,6 +26,8 @@ task Bcf2Vcf {
input {
File bcf
String outputPath = "./bcftools/SV.vcf"
+ String memory = "2G"
+ Int timeMinutes = 1 + ceil(size(bcf, "G"))
String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
}
@@ -40,12 +42,16 @@ task Bcf2Vcf {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
bcf: {description: "The generated BCF from an SV caller", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
diff --git a/bedtools.wdl b/bedtools.wdl
index 4f39e2a8907b3b8a713373a562e466905f727587..c228d6c6fb838f04f03a55f6729a8b8e08ceca9e 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -24,8 +24,10 @@ task Complement {
input {
File faidx
File inputBed
- String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
String outputBed = basename(inputBed, "\.bed") + ".complement.bed"
+ String memory = "~{512 + ceil(size([inputBed, faidx], "M"))}M"
+ Int timeMinutes = 1 + ceil(size([inputBed, faidx], "G"))
+ String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
# Use a fasta index file to get the genome sizes. And convert that to the
@@ -44,20 +46,19 @@ task Complement {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes",
- category: "required"}
- inputBed: {description: "The inputBed to complement",
- category: "required"}
- outputBed: {description: "The path to write the output to",
- category: "advanced"}
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes.", category: "required"}
+ inputBed: {description: "The inputBed to complement.", category: "required"}
+ outputBed: {description: "The path to write the output to.", category: "advanced"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
@@ -65,6 +66,8 @@ task Merge {
input {
File inputBed
String outputBed = "merged.bed"
+ String memory = "~{512 + ceil(size(inputBed, "M"))}M"
+ Int timeMinutes = 1 + ceil(size(inputBed, "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
@@ -77,18 +80,18 @@ task Merge {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- inputBed: {description: "The bed to merge",
- category: "required"}
- outputBed: {description: "The path to write the output to",
- category: "advanced"}
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ inputBed: {description: "The bed to merge.", category: "required"}
+ outputBed: {description: "The path to write the output to.", category: "advanced"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
@@ -97,6 +100,8 @@ task MergeBedFiles {
input {
Array[File]+ bedFiles
String outputBed = "merged.bed"
+ String memory = "~{512 + ceil(size(bedFiles, "M"))}M"
+ Int timeMinutes = 1 + ceil(size(bedFiles, "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
@@ -111,17 +116,17 @@ task MergeBedFiles {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- bedFiles: {description: "The bed files to merge",
- category: "required"}
- outputBed: {description: "The path to write the output to",
- category: "advanced"}
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ bedFiles: {description: "The bed files to merge.", category: "required"}
+ outputBed: {description: "The path to write the output to.", category: "advanced"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
@@ -172,6 +177,8 @@ task Intersect {
# Giving a faidx file will set the sorted option.
File? faidx
String outputBed = "intersect.bed"
+ String memory = "~{512 + ceil(size([regionsA, regionsB], "M"))}M"
+ Int timeMinutes = 1 + ceil(size([regionsA, regionsB], "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
Boolean sorted = defined(faidx)
@@ -192,21 +199,20 @@ task Intersect {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
faidx: {description: "The fasta index (.fai) file that is used to create the genome file required for sorted output. Implies sorted option.",
category: "common"}
- regionsA: {description: "Region file a to intersect",
- category: "required"}
- regionsB: {description: "Region file b to intersect",
- category: "required"}
- outputBed: {description: "The path to write the output to",
- category: "advanced"}
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ regionsA: {description: "Region file a to intersect", category: "required"}
+ regionsB: {description: "Region file b to intersect", category: "required"}
+ outputBed: {description: "The path to write the output to", category: "advanced"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
diff --git a/biopet/bamstats.wdl b/biopet/bamstats.wdl
index 7def9aec34b8d7adc50946922b86462739da5372..d71355d3a80dda92947992569b5d599944d3dc68 100644
--- a/biopet/bamstats.wdl
+++ b/biopet/bamstats.wdl
@@ -34,7 +34,7 @@ task Generate {
String outputDir
Reference? reference
- String memory = "16G"
+ String memory = "9G"
String javaXmx = "8G"
}
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index ec64fb4b4df2475c112e74e5c20e3401a1cecbce..cc8e1bc6382bb452c947403c0815804a1fcb3ede 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -31,7 +31,7 @@ task BaseCounter {
String outputDir
String prefix
- String memory = "14G"
+ String memory = "5G"
String javaXmx = "4G"
}
@@ -104,9 +104,10 @@ task ExtractAdaptersFastqc {
Float? adapterCutoff
Boolean? outputAsFasta
- String memory = "40G" # This is ridiculous, but needed due to vmem monitoring on SGE.
+ String memory = "9G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/biopet-extractadaptersfastqc:0.2--1"
+ Int timeMinutes = 5
}
command {
@@ -133,6 +134,7 @@ task ExtractAdaptersFastqc {
runtime {
memory: memory
docker: dockerImage
+ time_minutes: timeMinutes
}
}
@@ -143,7 +145,7 @@ task FastqSplitter {
Array[String]+ outputPaths
File? toolJar
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/biopet-fastqsplitter:0.1--2"
}
@@ -175,7 +177,7 @@ task FastqSync {
String out2path
File? toolJar
- String memory = "10G"
+ String memory = "5G"
String javaXmx = "4G"
}
@@ -208,52 +210,6 @@ task FastqSync {
}
}
-task ReorderGlobbedScatters {
- input {
- Array[File]+ scatters
-
- # Should not be changed from the main pipeline. As it should not influence results.
- # The 3.7-slim container is 143 mb on the filesystem. 3.7 is 927 mb.
- # The slim container is sufficient for this small task.
- String dockerImage = "python:3.7-slim"
- }
-
- command <<<
- set -e
- # Copy all the scatter files to the CWD so the output matches paths in
- # the cwd.
- for file in ~{sep=" " scatters}
- do cp $file .
- done
- python << CODE
- from os.path import basename
- scatters = ['~{sep="','" scatters}']
- splitext = [basename(x).split(".") for x in scatters]
- splitnum = [x.split("-") + [y] for x,y in splitext]
- ordered = sorted(splitnum, key=lambda x: int(x[1]))
- merged = ["{}-{}.{}".format(x[0],x[1],x[2]) for x in ordered]
- for x in merged:
- print(x)
- CODE
- >>>
-
- output {
- Array[File] reorderedScatters = read_lines(stdout())
- }
-
- runtime {
- docker: dockerImage
- # 4 gigs of memory to be able to build the docker image in singularity
- memory: "4G"
- }
-
- parameter_meta {
- scatters: {description: "The files which should be ordered.", category: "required"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
- }
-}
-
task ScatterRegions {
input {
File referenceFasta
@@ -264,8 +220,9 @@ task ScatterRegions {
File? bamFile
File? bamIndex
- String memory = "24G"
- String javaXmx = "8G"
+ String memory = "1G"
+ String javaXmx = "500M"
+ Int timeMinutes = 10
String dockerImage = "quay.io/biocontainers/biopet-scatterregions:0.2--0"
}
@@ -277,7 +234,7 @@ task ScatterRegions {
command <<<
set -e -o pipefail
mkdir -p ~{outputDirPath}
- biopet-scatterregions -Xmx~{javaXmx} \
+ biopet-scatterregions -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-R ~{referenceFasta} \
-o ~{outputDirPath} \
~{"-s " + scatterSize} \
@@ -306,6 +263,7 @@ task ScatterRegions {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -322,6 +280,7 @@ task ScatterRegions {
bamIndex: {description: "The index for the bamfile given through bamFile.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
@@ -335,7 +294,7 @@ task ValidateAnnotation {
File? gtfFile
Reference reference
- String memory = "9G"
+ String memory = "4G"
String javaXmx = "3G"
String dockerImage = "quay.io/biocontainers/biopet-validateannotation:0.1--0"
}
@@ -361,7 +320,7 @@ task ValidateFastq {
input {
File read1
File? read2
- String memory = "9G"
+ String memory = "4G"
String javaXmx = "3G"
String dockerImage = "quay.io/biocontainers/biopet-validatefastq:0.1.1--1"
}
@@ -386,7 +345,7 @@ task ValidateVcf {
input {
IndexedVcfFile vcf
Reference reference
- String memory = "9G"
+ String memory = "4G"
String javaXmx = "3G"
String dockerImage = "quay.io/biocontainers/biopet-validatevcf:0.1--0"
}
@@ -430,7 +389,7 @@ task VcfStats {
Array[String]+? sparkConfigValues
String dockerImage = "quay.io/biocontainers/biopet-vcfstats:1.2--0"
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
}
diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl
index 0fbd466a0ec1ee219f4785774c2231338c905d47..2b36952bdfe0ca9673c6d62478d0efab0c0f444c 100644
--- a/biopet/sampleconfig.wdl
+++ b/biopet/sampleconfig.wdl
@@ -34,7 +34,7 @@ task SampleConfig {
String? jsonOutputPath
String? tsvOutputPath
- String memory = "8G"
+ String memory = "17G"
String javaXmx = "16G"
}
@@ -74,7 +74,7 @@ task SampleConfigCromwellArrays {
Array[File]+ inputFiles
String outputPath
- String memory = "8G"
+ String memory = "5G"
String javaXmx = "4G"
}
@@ -110,7 +110,7 @@ task CaseControl {
String outputPath
String controlTag = "control"
- String memory = "8G"
+ String memory = "5G"
String javaXmx = "4G"
}
diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl
index 6694a75996ceb14cf8bc6b7671fe2a839ef8e8f6..e3a55ec3e7d50f219ef980fde482263a3d3f6670 100644
--- a/biopet/seqstat.wdl
+++ b/biopet/seqstat.wdl
@@ -32,7 +32,7 @@ task Generate {
String library
String readgroup
- String memory = "10G"
+ String memory = "5G"
String javaXmx = "4G"
}
diff --git a/biowdl.wdl b/biowdl.wdl
index 7aa68b271b73ac6c098fe1b0deffa6a06178b4a3..838755d911b42a729774c227d8521634c37c7b86 100644
--- a/biowdl.wdl
+++ b/biowdl.wdl
@@ -31,6 +31,8 @@ task InputConverter {
Boolean skipFileCheck=true
Boolean checkFileMd5sums=false
Boolean old=false
+
+ Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
}
@@ -50,6 +52,8 @@ task InputConverter {
}
runtime {
+ memory: "128M"
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -62,6 +66,7 @@ task InputConverter {
checkFileMd5sums: {description: "Whether or not the MD5 sums of the files mentioned in the samplesheet should be checked.",
category: "advanced"}
old: {description: "Whether or not the old samplesheet format should be used.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/bowtie.wdl b/bowtie.wdl
index 18fd6146adb6ea1b606f9d7b3bec6753d2c8fca4..b3f3ceaeadcc165cb2feec9d4e734f31e32c437c 100644
--- a/bowtie.wdl
+++ b/bowtie.wdl
@@ -37,7 +37,8 @@ task Bowtie {
String? samRG
Int threads = 1
- String memory = "16G"
+ Int timeMinutes = 1 + ceil(size(flatten([readsUpstream, readsDownstream]), "G") * 300 / threads)
+ String memory = "~{5 + ceil(size(indexFiles, "G"))}G"
String picardXmx = "4G"
# Image contains bowtie=1.2.2 and picard=2.9.2
String dockerImage = "quay.io/biocontainers/mulled-v2-bfe71839265127576d3cd749c056e7b168308d56:1d8bec77b352cdcf3e9ff3d20af238b33ed96eae-0"
@@ -78,6 +79,7 @@ task Bowtie {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -98,12 +100,8 @@ task Bowtie {
category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
-
-struct BowtieIndex {
- File fasta
- Array[File] indexFiles
-}
\ No newline at end of file
diff --git a/bwa.wdl b/bwa.wdl
index fec2b09f0b17279810759baabce7c5189833ee2d..3dd7883bd9920d83edd3d9250e9fbad29e496f51 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -29,8 +29,9 @@ task Mem {
String? readgroup
Int threads = 4
- String memory = "32G"
+ String memory = "~{5 + ceil(size(bwaIndex.indexFiles, "G"))}G"
String picardXmx = "4G"
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 200 / threads)
# A mulled container is needed to have both picard and bwa in one container.
# This container contains: picard (2.18.7), bwa (0.7.17-r1188)
String dockerImage = "quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0"
@@ -45,7 +46,7 @@ task Mem {
~{bwaIndex.fastaFile} \
~{read1} \
~{read2} \
- | picard -Xmx~{picardXmx} SortSam \
+ | picard -Xmx~{picardXmx} -XX:ParallelGCThreads=1 SortSam \
INPUT=/dev/stdin \
OUTPUT=~{outputPath} \
SORT_ORDER=coordinate \
@@ -60,6 +61,7 @@ task Mem {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -74,6 +76,7 @@ task Mem {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
picardXmx: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -96,7 +99,8 @@ task Kit {
# GATK/Picard default is level 2.
String sortMemoryPerThread = "4G"
Int compressionLevel = 1
- String memory = "32G"
+ String memory = "20G"
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biocontainers/bwakit:v0.7.15_cv1"
}
@@ -130,6 +134,7 @@ task Kit {
runtime {
cpu: threads + 1 # One thread for bwa-postalt + samtools.
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -146,6 +151,7 @@ task Kit {
sortMemoryPerThread: {description: "The amount of memory for each sorting thread.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
diff --git a/ccs.wdl b/ccs.wdl
index 3a8f887947faab7bc3ee898cf06fcd6ca28586d8..1762ac75decc526370ba83d46db018a9168c5da0 100644
--- a/ccs.wdl
+++ b/ccs.wdl
@@ -33,6 +33,7 @@ task CCS {
Int cores = 2
String memory = "2G"
+ Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/pbccs:4.2.0--0"
}
@@ -63,6 +64,7 @@ task CCS {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -78,6 +80,7 @@ task CCS {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 1fbc7be11726db716b2b9edd6b9b7b5528c74ac3..f2b26043de9becf264f1d136e2d5a39a1429c723 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -37,6 +37,7 @@ task Build {
Int threads = 5
String memory = "20G"
+ Int timeMinutes = 2880
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
@@ -64,6 +65,7 @@ task Build {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -82,6 +84,7 @@ task Build {
sizeTable: {description: "List of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", category: "common"}
threads: {description: "The number of threads to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -184,6 +187,7 @@ task Inspect {
Int? across
String memory = "4G"
+ Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
@@ -210,6 +214,7 @@ task Inspect {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -220,6 +225,7 @@ task Inspect {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
across: {description: "When printing FASTA output, output a newline character every <int> bases.", category: "common"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -307,6 +313,7 @@ task Kreport {
Int? minimumLength
String memory = "4G"
+ Int timeMinutes = 10
String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
@@ -335,6 +342,7 @@ task Kreport {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -349,6 +357,7 @@ task Kreport {
minimumScore: {description: "Require a minimum score for reads to be counted.", category: "advanced"}
minimumLength: {description: "Require a minimum alignment length to the read.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -362,6 +371,7 @@ task KTimportTaxonomy {
String outputPrefix
String memory = "4G"
+ Int timeMinutes = 1
String dockerImage = "biocontainers/krona:v2.7.1_cv1"
}
@@ -379,6 +389,7 @@ task KTimportTaxonomy {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -387,6 +398,7 @@ task KTimportTaxonomy {
inputFile: {description: "File with Centrifuge classification results.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/chunked-scatter.wdl b/chunked-scatter.wdl
index 619292d9f647bd76f30e29b07a8c08b84f4bf707..1b81687abda2b37851b8062eed02eb0420b458f0 100644
--- a/chunked-scatter.wdl
+++ b/chunked-scatter.wdl
@@ -28,6 +28,7 @@ task ChunkedScatter {
Int? overlap
Int? minimumBasesPerFile
+ Int timeMinutes = 2
String dockerImage = "quay.io/biocontainers/chunked-scatter:0.1.0--py_0"
}
@@ -48,6 +49,7 @@ task ChunkedScatter {
runtime {
memory: "4G"
+ time_minutes: timeMinutes
docker: dockerImage
}
diff --git a/clever.wdl b/clever.wdl
index e1dcf5a66401a21414cdd84c6087cee5933efebc..3a6515f721ff642ce3d91f7f8189db0b4542e2d7 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -37,6 +37,7 @@ task Mateclever {
Int threads = 10
String memory = "15G"
+ Int timeMinutes = 600
String dockerImage = "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
}
@@ -63,6 +64,7 @@ task Mateclever {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -78,6 +80,7 @@ task Mateclever {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
@@ -90,7 +93,8 @@ task Prediction {
String outputPath = "./clever"
Int threads = 10
- String memory = "15G"
+ String memory = "55G"
+ Int timeMinutes = 480
String dockerImage = "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
}
@@ -114,6 +118,7 @@ task Prediction {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -125,6 +130,7 @@ task Prediction {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/collect-columns.wdl b/collect-columns.wdl
index 8b1fa387d7bf277fc4832344beba48c2e5a5d667..e4e3a948dc8665dd34837a43e43a046fb40e7037 100644
--- a/collect-columns.wdl
+++ b/collect-columns.wdl
@@ -33,6 +33,8 @@ task CollectColumns {
File? referenceGtf
String? featureAttribute
+ Int memoryGb = 4 + ceil(0.5 * length(inputTables))
+ Int timeMinutes = 10
String dockerImage = "quay.io/biocontainers/collect-columns:0.2.0--py_1"
}
@@ -56,34 +58,25 @@ task CollectColumns {
File outputTable = outputPath
}
- Int memoryGb = 4 + ceil(0.5 * length(inputTables))
-
runtime {
memory: "~{memoryGb}G"
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- inputTables: {description: "The tables from which columns should be taken.",
- category: "required"}
- outputPath: {description: "The path to which the output should be written.",
- category: "required"}
- featureColumn: {description: "Equivalent to the -f option of collect-columns.",
- category: "advanced"}
- valueColumn: {description: "Equivalent to the -c option of collect-columns.",
- category: "advanced"}
- separator: {description: "Equivalent to the -s option of collect-columns.",
- category: "advanced"}
- sampleNames: {description: "Equivalent to the -n option of collect-columns.",
- category: "advanced"}
- header: {description: "Equivalent to the -H flag of collect-columns.",
- category: "advanced"}
- additionalAttributes: {description: "Equivalent to the -a option of collect-columns.",
- category: "advanced"}
- referenceGtf: {description: "Equivalent to the -g option of collect-columns.",
- category: "advanced"}
- featureAttribute: {description: "Equivalent to the -F option of collect-columns.",
- category: "advanced"}
+ inputTables: {description: "The tables from which columns should be taken.", category: "required"}
+ outputPath: {description: "The path to which the output should be written.", category: "required"}
+ featureColumn: {description: "Equivalent to the -f option of collect-columns.", category: "advanced"}
+ valueColumn: {description: "Equivalent to the -c option of collect-columns.", category: "advanced"}
+ separator: {description: "Equivalent to the -s option of collect-columns.", category: "advanced"}
+ sampleNames: {description: "Equivalent to the -n option of collect-columns.", category: "advanced"}
+ header: {description: "Equivalent to the -H flag of collect-columns.", category: "advanced"}
+ additionalAttributes: {description: "Equivalent to the -a option of collect-columns.", category: "advanced"}
+ referenceGtf: {description: "Equivalent to the -g option of collect-columns.", category: "advanced"}
+ featureAttribute: {description: "Equivalent to the -F option of collect-columns.", category: "advanced"}
+ memoryGb: {description: "The maximum amount of memory the job will need in GB", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/common.wdl b/common.wdl
index ef86abcc2c62b564fc23aeae227a2c95b4bfe652..f83255230874d77350b2d662e643f5e5e1f75aa2 100644
--- a/common.wdl
+++ b/common.wdl
@@ -179,10 +179,10 @@ task StringArrayMd5 {
}
task TextToFile {
-
input {
String text
String outputFile = "out.txt"
+ Int timeMinutes = 1
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
@@ -197,11 +197,13 @@ task TextToFile {
parameter_meta {
text: {description: "The text to print", category: "required"}
outputFile: {description: "The name of the output file", category: "common"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
runtime {
memory: "1G"
+ time_minutes: timeMinutes
docker: dockerImage
}
}
@@ -210,6 +212,9 @@ task YamlToJson {
input {
File yaml
String outputJson = basename(yaml, "\.ya?ml$") + ".json"
+
+ Int timeMinutes = 1
+ String memory = "128M"
# biowdl-input-converter has python and pyyaml.
String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
}
@@ -230,12 +235,16 @@ task YamlToJson {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
yaml: {description: "The YAML file to convert.", category: "required"}
outputJson: {description: "The location the output JSON file should be written to.", category: "advanced"}
+ memory: {description: "The maximum aount of memroy the job will need.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index d04865b618f61a4891bf753b64d1ad3f8bc11849..ad32ff21aff4958f9955628753a7b68468a855cd 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -79,7 +79,8 @@ task Cutadapt {
# Hence we use compression level 1 here.
Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
Int cores = 4
- String memory = "4G"
+ String memory = "~{300 + 100 * cores}M"
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
String dockerImage = "quay.io/biocontainers/cutadapt:2.8--py37h516909a_0"
}
@@ -167,231 +168,75 @@ task Cutadapt {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- read1: {
- description: "The first or single end fastq file to be run through cutadapt.",
- category: "required"
- }
- read2: {
- description: "An optional second end fastq file to be run through cutadapt.",
- category: "common"
- }
- read1output: {
- description: "The name of the resulting first or single end fastq file.",
- category: "common"
- }
- read2output: {
- description: "The name of the resulting second end fastq file.",
- category: "common"
- }
- adapter: {
- description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "common"
- }
- front: {
- description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "advanced"
- }
- anywhere: {
- description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
- category: "advanced"
- }
- adapterRead2: {
- description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "common"
- }
- frontRead2: {
- description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "advanced"
- }
- anywhereRead2: {
- description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
- category: "advanced"
- }
- interleaved: {
- description: "Equivalent to cutadapt's --interleaved flag.",
- category: "advanced"
- }
- pairFilter: {
- description: "Equivalent to cutadapt's --pair-filter option.",
- category: "advanced"
- }
- errorRate: {
- description: "Equivalent to cutadapt's --error-rate option.",
- category: "advanced"
- }
- noIndels: {
- description: "Equivalent to cutadapt's --no-indels flag.",
- category: "advanced"
- }
- times: {
- description: "Equivalent to cutadapt's --times option.",
- category: "advanced"
- }
- overlap: {
- description: "Equivalent to cutadapt's --overlap option.",
- category: "advanced"
- }
- matchReadWildcards: {
- description: "Equivalent to cutadapt's --match-read-wildcards flag.",
- category: "advanced"
- }
- noMatchAdapterWildcards: {
- description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.",
- category: "advanced"
- }
- noTrim: {
- description: "Equivalent to cutadapt's --no-trim flag.",
- category: "advanced"
- }
- maskAdapter: {
- description: "Equivalent to cutadapt's --mask-adapter flag.",
- category: "advanced"
- }
- cut: {
- description: "Equivalent to cutadapt's --cut option.",
- category: "advanced"
- }
- nextseqTrim: {
- description: "Equivalent to cutadapt's --nextseq-trim option.",
- category: "advanced"
- }
- qualityCutoff: {
- description: "Equivalent to cutadapt's --quality-cutoff option.",
- category: "advanced"
- }
- qualityBase: {
- description: "Equivalent to cutadapt's --quality-base option.",
- category: "advanced"
- }
- length: {
- description: "Equivalent to cutadapt's --length option.",
- category: "advanced"
- }
- trimN: {
- description: "Equivalent to cutadapt's --trim-n flag.",
- category: "advanced"
- }
- lengthTag: {
- description: "Equivalent to cutadapt's --length-tag option.",
- category: "advanced"
- }
- stripSuffix: {
- description: "Equivalent to cutadapt's --strip-suffix option.",
- category: "advanced"
- }
- prefix: {
- description: "Equivalent to cutadapt's --prefix option.",
- category: "advanced"
- }
- suffix: {
- description: "Equivalent to cutadapt's --suffix option.",
- category: "advanced"
- }
- minimumLength: {
- description: "Equivalent to cutadapt's --minimum-length option.",
- category: "advanced"
- }
- maximumLength: {
- description: "Equivalent to cutadapt's --maximum-length option.",
- category: "advanced"
- }
- maxN: {
- description: "Equivalent to cutadapt's --max-n option.",
- category: "advanced"
- }
- discardTrimmed: {
- description: "Equivalent to cutadapt's --quality-cutoff option.",
- category: "advanced"
- }
- discardUntrimmed: {
- description: "Equivalent to cutadapt's --discard-untrimmed option.",
- category: "advanced"
- }
- infoFilePath: {
- description: "Equivalent to cutadapt's --info-file option.",
- category: "advanced"
- }
- restFilePath: {
- description: "Equivalent to cutadapt's --rest-file option.",
- category: "advanced"
- }
- wildcardFilePath: {
- description: "Equivalent to cutadapt's --wildcard-file option.",
- category: "advanced"
- }
- tooShortOutputPath: {
- description: "Equivalent to cutadapt's --too-short-output option.",
- category: "advanced"
- }
- tooLongOutputPath: {
- description: "Equivalent to cutadapt's --too-long-output option.",
- category: "advanced"
- }
- untrimmedOutputPath: {
- description: "Equivalent to cutadapt's --untrimmed-output option.",
- category: "advanced"
- }
- tooShortPairedOutputPath: {
- description: "Equivalent to cutadapt's --too-short-paired-output option.",
- category: "advanced"
- }
- tooLongPairedOutputPath: {
- description: "Equivalent to cutadapt's --too-long-paired-output option.",
- category: "advanced"
- }
- untrimmedPairedOutputPath: {
- description: "Equivalent to cutadapt's --untrimmed-paired-output option.",
- category: "advanced"
- }
- colorspace: {
- description: "Equivalent to cutadapt's --colorspace flag.",
- category: "advanced"
- }
- doubleEncode: {
- description: "Equivalent to cutadapt's --double-encode flag.",
- category: "advanced"
- }
- stripF3: {
- description: "Equivalent to cutadapt's --strip-f3 flag.",
- category: "advanced"
- }
- maq: {
- description: "Equivalent to cutadapt's --maq flag.",
- category: "advanced"
- }
- bwa: {
- description: "Equivalent to cutadapt's --bwa flag.",
- category: "advanced"
- }
- zeroCap: {
- description: "Equivalent to cutadapt's --zero-cap flag.",
- category: "advanced"
- }
- noZeroCap: {
- description: "Equivalent to cutadapt's --no-zero-cap flag.",
- category: "advanced"
- }
- reportPath: {
- description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
- category: "common"
- }
- compressionLevel: {description: "The compression level if gzipped output is used.",
- category: "advanced"}
- cores: {
- description: "The number of cores to use.",
- category: "advanced"
- }
- memory: {
- description: "The amount of memory this job will use.",
- category: "advanced"
- }
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ read1: {description: "The first or single end fastq file to be run through cutadapt.", category: "required"}
+ read2: {description: "An optional second end fastq file to be run through cutadapt.", category: "common"}
+ read1output: {description: "The name of the resulting first or single end fastq file.", category: "common"}
+ read2output: {description: "The name of the resulting second end fastq file.", category: "common"}
+ adapter: {description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "common"}
+ front: {description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "advanced"}
+ anywhere: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "advanced"}
+ adapterRead2: {description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "common"}
+ frontRead2: {description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "advanced"}
+ anywhereRead2: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "advanced"}
+ interleaved: {description: "Equivalent to cutadapt's --interleaved flag.", category: "advanced"}
+ pairFilter: {description: "Equivalent to cutadapt's --pair-filter option.", category: "advanced"}
+ errorRate: {description: "Equivalent to cutadapt's --error-rate option.", category: "advanced"}
+ noIndels: {description: "Equivalent to cutadapt's --no-indels flag.", category: "advanced"}
+ times: {description: "Equivalent to cutadapt's --times option.", category: "advanced"}
+ overlap: {description: "Equivalent to cutadapt's --overlap option.", category: "advanced"}
+ matchReadWildcards: {description: "Equivalent to cutadapt's --match-read-wildcards flag.", category: "advanced"}
+ noMatchAdapterWildcards: {description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.", category: "advanced"}
+ noTrim: {description: "Equivalent to cutadapt's --no-trim flag.", category: "advanced"}
+ maskAdapter: {description: "Equivalent to cutadapt's --mask-adapter flag.", category: "advanced"}
+ cut: {description: "Equivalent to cutadapt's --cut option.", category: "advanced"}
+ nextseqTrim: {description: "Equivalent to cutadapt's --nextseq-trim option.", category: "advanced"}
+ qualityCutoff: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
+ qualityBase: {description: "Equivalent to cutadapt's --quality-base option.", category: "advanced"}
+ length: {description: "Equivalent to cutadapt's --length option.", category: "advanced"}
+ trimN: {description: "Equivalent to cutadapt's --trim-n flag.", category: "advanced"}
+ lengthTag: {description: "Equivalent to cutadapt's --length-tag option.", category: "advanced"}
+ stripSuffix: {description: "Equivalent to cutadapt's --strip-suffix option.", category: "advanced"}
+ prefix: {description: "Equivalent to cutadapt's --prefix option.", category: "advanced"}
+ suffix: {description: "Equivalent to cutadapt's --suffix option.", category: "advanced"}
+ minimumLength: {description: "Equivalent to cutadapt's --minimum-length option.", category: "advanced"}
+ maximumLength: {description: "Equivalent to cutadapt's --maximum-length option.", category: "advanced"}
+ maxN: {description: "Equivalent to cutadapt's --max-n option.", category: "advanced"}
+ discardTrimmed: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
+ discardUntrimmed: {description: "Equivalent to cutadapt's --discard-untrimmed option.", category: "advanced"}
+ infoFilePath: {description: "Equivalent to cutadapt's --info-file option.", category: "advanced"}
+ restFilePath: {description: "Equivalent to cutadapt's --rest-file option.", category: "advanced"}
+ wildcardFilePath: {description: "Equivalent to cutadapt's --wildcard-file option.", category: "advanced"}
+ tooShortOutputPath: {description: "Equivalent to cutadapt's --too-short-output option.", category: "advanced"}
+ tooLongOutputPath: {description: "Equivalent to cutadapt's --too-long-output option.", category: "advanced"}
+ untrimmedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-output option.", category: "advanced"}
+ tooShortPairedOutputPath: {description: "Equivalent to cutadapt's --too-short-paired-output option.", category: "advanced"}
+ tooLongPairedOutputPath: {description: "Equivalent to cutadapt's --too-long-paired-output option.", category: "advanced"}
+ untrimmedPairedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-paired-output option.", category: "advanced"}
+ colorspace: {description: "Equivalent to cutadapt's --colorspace flag.", category: "advanced"}
+ doubleEncode: {description: "Equivalent to cutadapt's --double-encode flag.", category: "advanced"}
+ stripF3: {description: "Equivalent to cutadapt's --strip-f3 flag.", category: "advanced"}
+ maq: {description: "Equivalent to cutadapt's --maq flag.", category: "advanced"}
+ bwa: {description: "Equivalent to cutadapt's --bwa flag.", category: "advanced"}
+ zeroCap: {description: "Equivalent to cutadapt's --zero-cap flag.", category: "advanced"}
+ noZeroCap: {description: "Equivalent to cutadapt's --no-zero-cap flag.", category: "advanced"}
+ reportPath: {description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
+ category: "common"}
+ compressionLevel: {description: "The compression level if gzipped output is used.", category: "advanced"}
+ cores: {description: "The number of cores to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
diff --git a/delly.wdl b/delly.wdl
index ad8f18d9579d35ab161499cfd70cf28742fa1ce6..efa1bf60d7be4483f00607c66250b8247d49b7e0 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -31,6 +31,7 @@ task CallSV {
String outputPath = "./delly/delly.vcf"
String memory = "15G"
+ Int timeMinutes = 300
String dockerImage = "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
}
@@ -49,6 +50,7 @@ task CallSV {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -60,6 +62,7 @@ task CallSV {
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 4d10147cc8cbbc404a095be85603322452a384ee..e24b6ce44afcc62d95e752bddf88401c48e4bb6b 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -38,7 +38,9 @@ task Fastqc {
String? dir
Int threads = 1
- String memory = "4G"
+ # Fastqc uses 250MB per thread in its wrapper.
+ String memory = "~{250 + 250 * threads}M"
+ Int timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
Array[File]? NoneArray
File? NoneFile
@@ -84,6 +86,7 @@ task Fastqc {
cpu: threads
memory: memory
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -103,6 +106,7 @@ task Fastqc {
dir: {description: "Equivalent to fastqc's --dir option.", category: "advanced"}
threads: {description: "The number of cores to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -116,6 +120,7 @@ task Fastqc {
task GetConfiguration {
input {
+ Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4"
}
@@ -138,13 +143,13 @@ task GetConfiguration {
runtime {
memory: "2G" # Needs more than 1 to pull the docker image
+ time_minute: timeMinutes
docker: dockerImage
}
parameter_meta {
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
diff --git a/gatk.wdl b/gatk.wdl
index 586c25d09edfde9cb6efa6387c445fb8b37753e9..edafc4d4cc9a4acb24bbcd5b385ab7e628cf7966 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -32,15 +32,16 @@ task AnnotateIntervals {
File? segmentalDuplicationTrack
Int featureQueryLookahead = 1000000
- String memory = "10G"
+ String memory = "3G"
String javaXmx = "2G"
+ Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{annotatedIntervalsPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
AnnotateIntervals \
-R ~{referenceFasta} \
-L ~{intervals} \
@@ -57,6 +58,7 @@ task AnnotateIntervals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -73,6 +75,7 @@ task AnnotateIntervals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -90,15 +93,16 @@ task ApplyBQSR {
File referenceFastaDict
File referenceFastaFai
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
@@ -121,6 +125,7 @@ task ApplyBQSR {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -139,6 +144,7 @@ task ApplyBQSR {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -159,15 +165,16 @@ task BaseRecalibrator {
File referenceFastaDict
File referenceFastaFai
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{recalibrationReportPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
BaseRecalibrator \
-R ~{referenceFasta} \
-I ~{inputBam} \
@@ -184,6 +191,7 @@ task BaseRecalibrator {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -205,6 +213,7 @@ task BaseRecalibrator {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -215,14 +224,15 @@ task CalculateContamination {
File tumorPileups
File? normalPileups
- String memory = "24G"
+ String memory = "13G"
String javaXmx = "12G"
+ Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CalculateContamination \
-I ~{tumorPileups} \
~{"-matched " + normalPileups} \
@@ -237,6 +247,7 @@ task CalculateContamination {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -246,6 +257,7 @@ task CalculateContamination {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -256,15 +268,16 @@ task CallCopyRatioSegments {
String outputPrefix
File copyRatioSegments
- String memory = "21G"
- String javaXmx = "6G"
+ String memory = "3G"
+ String javaXmx = "2G"
+ Int timeMinutes = 2
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CallCopyRatioSegments \
-I ~{copyRatioSegments} \
-O ~{outputPrefix}.called.seg
@@ -277,6 +290,7 @@ task CallCopyRatioSegments {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -286,6 +300,7 @@ task CallCopyRatioSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -301,15 +316,17 @@ task CollectAllelicCounts {
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- String memory = "90G"
- String javaXmx = "30G"
+
+ String memory = "11G"
+ String javaXmx = "10G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{allelicCountsPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CollectAllelicCounts \
-L ~{commonVariantSites} \
-I ~{inputBam} \
@@ -323,6 +340,7 @@ task CollectAllelicCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -338,6 +356,7 @@ task CollectAllelicCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -354,15 +373,16 @@ task CollectReadCounts {
File referenceFastaFai
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "35G"
+ String memory = "8G"
String javaXmx = "7G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 5)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{countsPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CollectReadCounts \
-L ~{intervals} \
-I ~{inputBam} \
@@ -378,6 +398,7 @@ task CollectReadCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -393,6 +414,7 @@ task CollectReadCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -408,15 +430,16 @@ task CombineGVCFs {
File referenceFastaDict
File referenceFastaFai
- String memory = "24G"
- String javaXmx = "12G"
+ String memory = "5G"
+ String javaXmx = "4G"
+ Int timeMinutes = 1 + ceil(size(gvcfFiles, "G") * 8)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CombineGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
@@ -431,6 +454,7 @@ task CombineGVCFs {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -448,6 +472,7 @@ task CombineGVCFs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -465,8 +490,9 @@ task CombineVariants {
Array[File]+ variantIndexes
String outputPath
- String memory = "24G"
+ String memory = "13G"
String javaXmx = "12G"
+ Int timeMinutes = 180
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
@@ -485,7 +511,7 @@ task CombineVariants {
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
done
')
- java -Xmx~{javaXmx} -jar /usr/GenomeAnalysisTK.jar \
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 -jar /usr/GenomeAnalysisTK.jar \
-T CombineVariants \
-R ~{referenceFasta} \
--genotypemergeoption ~{genotypeMergeOption} \
@@ -501,6 +527,7 @@ task CombineVariants {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -518,6 +545,7 @@ task CombineVariants {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -529,15 +557,16 @@ task CreateReadCountPanelOfNormals {
Array[File]+ readCountsFiles
File? annotatedIntervals
- String memory = "21G"
+ String memory = "8G"
String javaXmx = "7G"
+ Int timeMinutes = 5
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer causes a spark related error for some reason...
}
command {
set -e
mkdir -p "$(dirname ~{PONpath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
CreateReadCountPanelOfNormals \
-I ~{sep=" -I " readCountsFiles} \
~{"--annotated-intervals " + annotatedIntervals} \
@@ -550,6 +579,7 @@ task CreateReadCountPanelOfNormals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -561,6 +591,7 @@ task CreateReadCountPanelOfNormals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -573,15 +604,16 @@ task DenoiseReadCounts {
File readCounts
String outputPrefix
- String memory = "39G"
- String javaXmx = "13G"
+ String memory = "5G"
+ String javaXmx = "4G"
+ Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
DenoiseReadCounts \
-I ~{readCounts} \
~{"--count-panel-of-normals " + PON} \
@@ -597,6 +629,7 @@ task DenoiseReadCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -609,6 +642,7 @@ task DenoiseReadCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -628,15 +662,16 @@ task FilterMutectCalls {
Int uniqueAltReadCount = 4
File mutect2Stats
- String memory = "24G"
+ String memory = "13G"
String javaXmx = "12G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(dirname ~{outputVcf})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
FilterMutectCalls \
-R ~{referenceFasta} \
-V ~{unfilteredVcf} \
@@ -658,6 +693,7 @@ task FilterMutectCalls {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -677,6 +713,7 @@ task FilterMutectCalls {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -688,15 +725,16 @@ task GatherBqsrReports {
Array[File] inputBQSRreports
String outputReportPath
- String memory = "12G"
- String javaXmx = "4G"
+ String memory = "1G"
+ String javaXmx = "500M"
+ Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputReportPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
@@ -708,6 +746,7 @@ task GatherBqsrReports {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -718,6 +757,7 @@ task GatherBqsrReports {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -731,15 +771,16 @@ task GenomicsDBImport {
String genomicsDBWorkspacePath = "genomics_db"
String genomicsDBTarFile = "genomics_db.tar.gz"
String? tmpDir
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{genomicsDBWorkspacePath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
GenomicsDBImport \
-V ~{sep=" -V " gvcfFiles} \
--genomicsdb-workspace-path ~{genomicsDBWorkspacePath} \
@@ -754,6 +795,7 @@ task GenomicsDBImport {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -764,10 +806,11 @@ task GenomicsDBImport {
genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored", category: "advanced"}
genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored", category: "advanced"}
tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers",
- category: "advanced"}
+ category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -787,15 +830,16 @@ task GenotypeGVCFs {
File? dbsnpVCFIndex
File? pedigree
- String memory = "18G"
+ String memory = "7G"
String javaXmx = "6G"
+ Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
GenotypeGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
@@ -815,6 +859,7 @@ task GenotypeGVCFs {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -835,6 +880,7 @@ task GenotypeGVCFs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -850,14 +896,15 @@ task GetPileupSummaries {
File sitesForContaminationIndex
String outputPrefix
- String memory = "24G"
+ String memory = "13G"
String javaXmx = "12G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
GetPileupSummaries \
-I ~{sampleBam} \
-V ~{variantsForContamination} \
@@ -871,6 +918,7 @@ task GetPileupSummaries {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -886,6 +934,7 @@ task GetPileupSummaries {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -913,15 +962,16 @@ task HaplotypeCaller {
Boolean dontUseSoftClippedBases = false
Float? standardMinConfidenceThresholdForCalling
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 400 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
HaplotypeCaller \
-R ~{referenceFasta} \
-O ~{outputPath} \
@@ -945,6 +995,7 @@ task HaplotypeCaller {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -974,6 +1025,7 @@ task HaplotypeCaller {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -984,14 +1036,15 @@ task LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
- String memory = "24G"
+ String memory = "13G"
String javaXmx = "12G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
LearnReadOrientationModel \
-I ~{sep=" -I " f1r2TarGz} \
-O "artifact-priors.tar.gz"
@@ -1003,6 +1056,7 @@ task LearnReadOrientationModel {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1011,6 +1065,7 @@ task LearnReadOrientationModel {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1020,14 +1075,15 @@ task MergeStats {
input {
Array[File]+ stats
- String memory = "28G"
+ String memory = "15G"
String javaXmx = "14G"
+ Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
MergeMutectStats \
-stats ~{sep=" -stats " stats} \
-O "merged.stats"
@@ -1039,6 +1095,7 @@ task MergeStats {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1047,6 +1104,7 @@ task MergeStats {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1064,15 +1122,16 @@ task ModelSegments {
else 30
Int maximumNumberOfSmoothingIterations = 10
- String memory = "64G"
+ String memory = "11G"
String javaXmx = "10G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p ~{outputDir}
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
ModelSegments \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
@@ -1099,6 +1158,7 @@ task ModelSegments {
runtime {
docker: dockerImage
+ time_minute: timeMinutes
memory: memory
}
@@ -1114,6 +1174,7 @@ task ModelSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1137,15 +1198,16 @@ task MuTect2 {
Array[File]+ intervals
String outputStats = outputVcf + ".stats"
- String memory = "16G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 240
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputVcf})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
Mutect2 \
-R ~{referenceFasta} \
-I ~{sep=" -I " inputBams} \
@@ -1167,6 +1229,7 @@ task MuTect2 {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1189,6 +1252,7 @@ task MuTect2 {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1203,15 +1267,16 @@ task PlotDenoisedCopyRatios {
File denoisedCopyRatios
Int? minimumContigLength
- String memory = "32G"
- String javaXmx = "7G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
command {
set -e
mkdir -p ~{outputDir}
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
PlotDenoisedCopyRatios \
--standardized-copy-ratios ~{standardizedCopyRatios} \
--denoised-copy-ratios ~{denoisedCopyRatios} \
@@ -1232,6 +1297,7 @@ task PlotDenoisedCopyRatios {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1245,6 +1311,7 @@ task PlotDenoisedCopyRatios {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1260,15 +1327,16 @@ task PlotModeledSegments {
File allelicCounts
Int? minimumContigLength
- String memory = "21G"
- String javaXmx = "7G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
command {
set -e
mkdir -p ~{outputDir}
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
PlotModeledSegments \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
@@ -1285,6 +1353,7 @@ task PlotModeledSegments {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1299,6 +1368,7 @@ task PlotModeledSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1315,15 +1385,16 @@ task PreprocessIntervals {
Int padding = if defined(intervals) then 250 else 0
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "10G"
- String javaXmx = "2G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 6)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputIntervalList})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
PreprocessIntervals \
-R ~{referenceFasta} \
--sequence-dictionary ~{referenceFastaDict} \
@@ -1340,6 +1411,7 @@ task PreprocessIntervals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1355,6 +1427,7 @@ task PreprocessIntervals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1370,15 +1443,16 @@ task SelectVariants {
String outputPath = "output.vcf.gz"
String? selectTypeToInclude
Array[File] intervals = []
- String memory = "16G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
SelectVariants \
-R ~{referenceFasta} \
-V ~{inputVcf} \
@@ -1394,6 +1468,7 @@ task SelectVariants {
runtime {
docker: dockerImage
+ time_minute: timeMinutes
memory: memory
}
@@ -1412,6 +1487,7 @@ task SelectVariants {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1427,15 +1503,16 @@ task SplitNCigarReads {
String outputBam
Array[File] intervals = []
- String memory = "16G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputBam})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
SplitNCigarReads \
-I ~{inputBam} \
-R ~{referenceFasta} \
@@ -1450,6 +1527,7 @@ task SplitNCigarReads {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1467,6 +1545,7 @@ task SplitNCigarReads {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1483,15 +1562,16 @@ task VariantFiltration {
Array[String]+ filterArguments
Array[File] intervals = []
- String memory = "16G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- gatk --java-options -Xmx~{javaXmx} \
+ gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
VariantFiltration \
-I ~{inputVcf} \
-R ~{referenceFasta} \
@@ -1507,6 +1587,7 @@ task VariantFiltration {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1525,6 +1606,7 @@ task VariantFiltration {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index ca2b1669d64c2fe95c7068df00a8445fa9f6e21a..e5f62b5ec557ef05afbfcee0bb24d175a2b316b6 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -44,6 +44,7 @@ task GffCompare {
Boolean verbose = false
Boolean debugMode = false
+ Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
# This workaround only works in the input section.
@@ -107,9 +108,11 @@ task GffCompare {
File? missedIntrons = if debugMode
then totalPrefix + ".missed_introns.gtf"
else noneFile
+ Array[File] allFiles = select_all([annotated, loci, stats, tracking, redundant, missedIntrons])
}
runtime {
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -134,6 +137,7 @@ task GffCompare {
noTmap: {description: "Equivalent to gffcompare's `-T` flag.", category: "advanced"}
verbose: {description: "Equivalent to gffcompare's `-V` flag.", category: "advanced"}
debugMode: {description: "Equivalent to gffcompare's `-D` flag.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/gffread.wdl b/gffread.wdl
index 6b23785c7ee37c0fb112ed59d45424d2bced07d0..d83e4d76564411d1edd8b3ef5a17ac208f8bad67 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -30,6 +30,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
Boolean outputGtfFormat = false
+ Int timeMinutes = 1 + ceil(size(inputGff) * 10)
String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
@@ -62,6 +63,7 @@ task GffRead {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -73,6 +75,7 @@ task GffRead {
proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"}
filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"}
outputGtfFormat: {description: "Equivalent to gffread's `-T` flag.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/hisat2.wdl b/hisat2.wdl
index b65b2da95379e83363654fc6a58893586ed4ee12..85bd3b353f4cc6c788b6530c25afd8c9c4606177 100644
--- a/hisat2.wdl
+++ b/hisat2.wdl
@@ -33,8 +33,9 @@ task Hisat2 {
Boolean downstreamTranscriptomeAssembly = true
String summaryFilePath = basename(outputBam, ".bam") + ".summary.txt"
- Int threads = 1
- String memory = "48G"
+ Int threads = 4
+ String memory = "~{threads + 5 + ceil(size(indexFiles, "G"))}G"
+ Int timeMinutes = 1 + ceil(size([inputR1, inputR2], "G") * 180 / threads)
# quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
# is a combination of hisat2 and samtools
# hisat2=2.1.0, samtools=1.8
@@ -56,7 +57,8 @@ task Hisat2 {
--rg 'LB:~{library}' \
--rg 'PL:~{platform}' \
~{true="--dta" false="" downstreamTranscriptomeAssembly} \
- --new-summary ~{summaryFilePath} \
+ --new-summary \
+ --summary-file ~{summaryFilePath} \
| samtools sort > ~{outputBam}
samtools index ~{outputBam} ~{bamIndexPath}
}
@@ -70,6 +72,7 @@ task Hisat2 {
runtime {
memory: memory
cpu: threads + 1
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -85,6 +88,7 @@ task Hisat2 {
downstreamTranscriptomeAssembly: {description: "Equivalent to hisat2's `--dta` flag.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/htseq.wdl b/htseq.wdl
index 900a88a79b96fab968b1244d0b3d6e090db70df5..35faeef3a1158634cfdbff45f663bab9d40d035e 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -33,6 +33,7 @@ task HTSeqCount {
Array[String] additionalAttributes = []
String memory = "40G"
+ Int timeMinutes = 10 + ceil(size(inputBams, "G") * 60)
String dockerImage = "quay.io/biocontainers/htseq:0.11.2--py37h637b7d7_1"
}
@@ -56,54 +57,24 @@ task HTSeqCount {
}
runtime {
+ time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
parameter_meta {
- inputBams: {
- description: "The input BAM files.",
- category: "required"
- }
- gtfFile: {
- description: "A GTF/GFF file containing the features of interest.",
- category: "required"
- }
- outputTable: {
- description: "The path to which the output table should be written.",
- category: "common"
- }
- format: {
- description: "Equivalent to the -f option of htseq-count.",
- category: "advanced"
- }
- order: {
- description: "Equivalent to the -r option of htseq-count.",
- category: "advanced"
- }
- stranded: {
- description: "Equivalent to the -s option of htseq-count.",
- category: "common"
- }
- featureType: {
- description: "Equivalent to the --type option of htseq-count.",
- category: "advanced"
- }
- idattr: {
- description: "Equivalent to the --idattr option of htseq-count.",
- category: "advanced"
- }
- additionalAttributes: {
- description: "Equivalent to the --additional-attr option of htseq-count.",
- category: "advanced"
- }
- memory: {
- description: "The amount of memory the job requires in GB.",
- category: "advanced"
- }
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ inputBams: {description: "The input BAM files.", category: "required"}
+ gtfFile: {description: "A GTF/GFF file containing the features of interest.", category: "required"}
+ outputTable: {description: "The path to which the output table should be written.", category: "common"}
+ format: {description: "Equivalent to the -f option of htseq-count.", category: "advanced"}
+ order: {description: "Equivalent to the -r option of htseq-count.", category: "advanced"}
+ stranded: {description: "Equivalent to the -s option of htseq-count.", category: "common"}
+ featureType: {description: "Equivalent to the --type option of htseq-count.", category: "advanced"}
+ idattr: {description: "Equivalent to the --idattr option of htseq-count.", category: "advanced"}
+ additionalAttributes: {description: "Equivalent to the --additional-attr option of htseq-count.", category: "advanced"}
+ memory: {description: "The amount of memory the job requires in GB.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
diff --git a/isoseq3.wdl b/isoseq3.wdl
index 10d87bbc2264ac1aad7661f8ab8786249503684a..9e0dfdb2f43d4ba4ea2dd1807eb152ece5a15446 100644
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -32,6 +32,7 @@ task Refine {
Int cores = 2
String memory = "2G"
+ Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
}
@@ -61,6 +62,7 @@ task Refine {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -75,6 +77,7 @@ task Refine {
outputNamePrefix: {description: "Basename of the output files.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/lima.wdl b/lima.wdl
index ba8a5407fa1be7757beaff0b5bdb404016793352..ddd37da4237296c40349fa4d6b3b553924fbaadd 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -50,6 +50,7 @@ task Lima {
Int cores = 2
String memory = "2G"
+ Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
}
@@ -110,6 +111,7 @@ task Lima {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -142,6 +144,7 @@ task Lima {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/manta.wdl b/manta.wdl
index 5006a01efb5d92a97d527fa26b5866db959c3329..5382d2a5b6ad067efe9ba395ff7ab48077630f83 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -33,6 +33,7 @@ task Germline {
Int cores = 1
Int memoryGb = 4
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
@@ -60,6 +61,7 @@ task Germline {
cpu: cores
memory: "~{memoryGb}G"
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -74,6 +76,7 @@ task Germline {
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The the number of cores required to run a program", category: "required"}
memoryGb: {description: "The memory required to run the manta", category: "required"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
@@ -93,6 +96,7 @@ task Somatic {
Int cores = 1
Int memoryGb = 4
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
@@ -130,6 +134,7 @@ task Somatic {
cpu: cores
memory: "~{memoryGb}G"
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -145,6 +150,7 @@ task Somatic {
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
diff --git a/minimap2.wdl b/minimap2.wdl
index fd28d4a9b0eed78dd8c52db211f1eea81246f1da..04b02bf2bdc7454c8e7c772063f1999e672a4d30 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -32,6 +32,7 @@ task Indexing {
Int cores = 1
String memory = "4G"
+ Int timeMinutes = 10
String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
}
@@ -55,6 +56,7 @@ task Indexing {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -68,6 +70,7 @@ task Indexing {
splitIndex: {description: "Split index for every ~NUM input bases.", category: "advanced"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# output
@@ -96,6 +99,7 @@ task Mapping {
Int cores = 4
String memory = "30G"
+ Int timeMinutes = 1 + ceil(size(queryFile, "G") * 200 / cores)
String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
}
@@ -128,6 +132,7 @@ task Mapping {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -149,6 +154,7 @@ task Mapping {
queryFile: {description: "Input fasta file.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# output
diff --git a/multiqc.wdl b/multiqc.wdl
index b50122e0a51b7fd714407ca692377af314f901ce..62ca5421cfb6e3062fc0997be6ca8fa605207302 100644
--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -53,7 +53,7 @@ task MultiQC {
String? clConfig
String memory = "4G"
-
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/multiqc:1.7--py_1"
}
@@ -133,6 +133,7 @@ task MultiQC {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -170,6 +171,7 @@ task MultiQC {
finished: {description: "An array of booleans that can be used to let multiqc wait on stuff.", category: "internal_use_only"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/picard.wdl b/picard.wdl
index e92755045485b108a502025e5d2f6112ccc40264..3103ad9baa7287a211a652e892dfa45a1071bebc 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -26,15 +26,16 @@ task BedToIntervalList {
File dict
String outputPath = "regions.interval_list"
- String memory = "12G"
- String javaXmx = "4G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
BedToIntervalList \
I=~{bedFile} \
O=~{outputPath} \
@@ -47,6 +48,7 @@ task BedToIntervalList {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -54,11 +56,11 @@ task BedToIntervalList {
# inputs
bedFile: {description: "A bed file.", category: "required"}
dict: {description: "A sequence dict file.", category: "required"}
- outputPath: {description: "The location the output interval list should be written to.",
- category: "advanced"}
+ outputPath: {description: "The location the output interval list should be written to.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -83,8 +85,9 @@ task CollectMultipleMetrics {
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
- String memory = "32G"
+ String memory = "9G"
String javaXmx = "8G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -92,7 +95,7 @@ task CollectMultipleMetrics {
command {
set -e
mkdir -p "$(dirname ~{basename})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
CollectMultipleMetrics \
I=~{inputBam} \
R=~{referenceFasta} \
@@ -110,24 +113,24 @@ task CollectMultipleMetrics {
}
output {
- File alignmentSummary = basename + ".alignment_summary_metrics"
- File baitBiasDetail = basename + ".bait_bias_detail_metrics"
- File baitBiasSummary = basename + ".bait_bias_summary_metrics"
- File baseDistributionByCycle = basename + ".base_distribution_by_cycle_metrics"
+ File? alignmentSummary = basename + ".alignment_summary_metrics"
+ File? baitBiasDetail = basename + ".bait_bias_detail_metrics"
+ File? baitBiasSummary = basename + ".bait_bias_summary_metrics"
+ File? baseDistributionByCycle = basename + ".base_distribution_by_cycle_metrics"
File? baseDistributionByCyclePdf = basename + ".base_distribution_by_cycle.pdf"
- File errorSummary = basename + ".error_summary_metrics"
- File gcBiasDetail = basename + ".gc_bias.detail_metrics"
- File gcBiasPdf = basename + ".gc_bias.pdf"
- File gcBiasSummary = basename + ".gc_bias.summary_metrics"
+ File? errorSummary = basename + ".error_summary_metrics"
+ File? gcBiasDetail = basename + ".gc_bias.detail_metrics"
+ File? gcBiasPdf = basename + ".gc_bias.pdf"
+ File? gcBiasSummary = basename + ".gc_bias.summary_metrics"
File? insertSizeHistogramPdf = basename + ".insert_size_histogram.pdf"
File? insertSize = basename + ".insert_size_metrics"
- File preAdapterDetail = basename + ".pre_adapter_detail_metrics"
- File preAdapterSummary = basename + ".pre_adapter_summary_metrics"
- File qualityByCycle = basename + ".quality_by_cycle_metrics"
+ File? preAdapterDetail = basename + ".pre_adapter_detail_metrics"
+ File? preAdapterSummary = basename + ".pre_adapter_summary_metrics"
+ File? qualityByCycle = basename + ".quality_by_cycle_metrics"
File? qualityByCyclePdf = basename + ".quality_by_cycle.pdf"
- File qualityDistribution = basename + ".quality_distribution_metrics"
+ File? qualityDistribution = basename + ".quality_distribution_metrics"
File? qualityDistributionPdf = basename + ".quality_distribution.pdf"
- File qualityYield = basename + ".quality_yield_metrics"
+ File? qualityYield = basename + ".quality_yield_metrics"
# Using a glob is easier. But will lead to very ugly output directories.
Array[File] allStats = select_all([
alignmentSummary,
@@ -153,33 +156,29 @@ task CollectMultipleMetrics {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
parameter_meta {
# inputs
- inputBam: {description: "The input BAM file for which metrics will be collected.",
- category: "required"}
+ inputBam: {description: "The input BAM file for which metrics will be collected.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
- basename: {description: "The basename/prefix of the output files (may include directories).",
- category: "required"}
+ basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
collectAlignmentSummaryMetrics: {description: "Equivalent to the `PROGRAM=CollectAlignmentSummaryMetrics` argument.",
category: "advanced"}
collectInsertSizeMetrics: {description: "Equivalent to the `PROGRAM=CollectInsertSizeMetrics` argument.",
category: "advanced"}
qualityScoreDistribution: {description: "Equivalent to the `PROGRAM=QualityScoreDistribution` argument.",
category: "advanced"}
- meanQualityByCycle: {description: "Equivalent to the `PROGRAM=MeanQualityByCycle` argument.",
- category: "advanced"}
+ meanQualityByCycle: {description: "Equivalent to the `PROGRAM=MeanQualityByCycle` argument.", category: "advanced"}
collectBaseDistributionByCycle: {description: "Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.",
category: "advanced"}
- collectGcBiasMetrics: {description: "Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.",
- category: "advanced"}
+ collectGcBiasMetrics: {description: "Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.", category: "advanced"}
collectSequencingArtifactMetrics: {description: "Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.",
category: "advanced"}
collectQualityYieldMetrics: {description: "Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.",
@@ -188,6 +187,7 @@ task CollectMultipleMetrics {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -201,8 +201,9 @@ task CollectRnaSeqMetrics {
String basename
String strandSpecificity = "NONE"
- String memory = "32G"
+ String memory = "9G"
String javaXmx = "8G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -210,7 +211,7 @@ task CollectRnaSeqMetrics {
set -e
mkdir -p "$(dirname ~{basename})"
picard -Xmx~{javaXmx} \
- CollectRnaSeqMetrics \
+ CollectRnaSeqMetrics -XX:ParallelGCThreads=1 \
I=~{inputBam} \
O=~{basename}.RNA_Metrics \
CHART_OUTPUT=~{basename}.RNA_Metrics.pdf \
@@ -225,23 +226,23 @@ task CollectRnaSeqMetrics {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
parameter_meta {
# inputs
- inputBam: {description: "The input BAM file for which metrics will be collected.",
- category: "required"}
+ inputBam: {description: "The input BAM file for which metrics will be collected.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
refRefflat: {description: "A refflat file containing gene annotations.", catehory: "required"}
- basename: {description: "The basename/prefix of the output files (may include directories).",
- category: "required"}
+ basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics.",
category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -258,15 +259,16 @@ task CollectTargetedPcrMetrics {
Array[File]+ targetIntervals
String basename
- String memory = "12G"
- String javaXmx = "4G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p "$(dirname ~{basename})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
CollectTargetedPcrMetrics \
I=~{inputBam} \
R=~{referenceFasta} \
@@ -285,16 +287,15 @@ task CollectTargetedPcrMetrics {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
parameter_meta {
# inputs
- inputBam: {description: "The input BAM file for which metrics will be collected.",
- category: "required"}
+ inputBam: {description: "The input BAM file for which metrics will be collected.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
- referenceFasta: {description: "The reference fasta file which was also used for mapping.",
- category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
@@ -302,12 +303,12 @@ task CollectTargetedPcrMetrics {
category: "required"}
targetIntervals: {description: "An interval list describing the coordinates of the targets sequenced.",
category: "required"}
- basename: {description: "The basename/prefix of the output files (may include directories).",
- category: "required"}
+ basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -362,15 +363,16 @@ task GatherBamFiles {
Array[File]+ inputBamsIndex
String outputBamPath
- String memory = "12G"
- String javaXmx = "4G"
+ String memory = "4G"
+ String javaXmx = "3G"
+ Int timeMinutes = 1 + ceil(size(inputBams, "G") * 0.5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
GatherBamFiles \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
@@ -386,6 +388,7 @@ task GatherBamFiles {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -398,6 +401,7 @@ task GatherBamFiles {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -409,15 +413,16 @@ task GatherVcfs {
Array[File]+ inputVcfIndexes
String outputVcfPath = "out.vcf.gz"
- String memory = "12G"
+ String memory = "5G"
String javaXmx = "4G"
+ Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputVcfPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
GatherVcfs \
INPUT=~{sep=' INPUT=' inputVcfs} \
OUTPUT=~{outputVcfPath}
@@ -430,6 +435,7 @@ task GatherVcfs {
runtime {
docker: dockerImage
memory: memory
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -441,6 +447,7 @@ task GatherVcfs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -454,8 +461,9 @@ task MarkDuplicates {
String outputBamPath
String metricsPath
- String memory = "24G"
+ String memory = "9G"
String javaXmx = "8G"
+ Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
@@ -473,7 +481,7 @@ task MarkDuplicates {
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
MarkDuplicates \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
@@ -496,6 +504,7 @@ task MarkDuplicates {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -510,6 +519,7 @@ task MarkDuplicates {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -522,8 +532,9 @@ task MergeVCFs {
Array[File]+ inputVCFsIndexes
String outputVcfPath
- String memory = "24G"
- String javaXmx = "8G"
+ String memory = "5G"
+ String javaXmx = "4G"
+ Int timeMinutes = 1 + ceil(size(inputVCFs, "G"))
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -533,7 +544,7 @@ task MergeVCFs {
command {
set -e
mkdir -p "$(dirname ~{outputVcfPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
MergeVcfs \
INPUT=~{sep=' INPUT=' inputVCFs} \
OUTPUT=~{outputVcfPath}
@@ -546,6 +557,7 @@ task MergeVCFs {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -558,6 +570,7 @@ task MergeVCFs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -569,7 +582,7 @@ task SamToFastq {
File inputBamIndex
Boolean paired = true
- String memory = "48G"
+ String memory = "17G"
String javaXmx = "16G" # High memory default to avoid crashes.
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
File? NONE
@@ -581,7 +594,7 @@ task SamToFastq {
command {
set -e
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
SamToFastq \
I=~{inputBam} \
~{"FASTQ=" + outputRead1} \
@@ -606,15 +619,15 @@ task ScatterIntervalList {
File interval_list
Int scatter_count
- String memory = "12G"
- String javaXmx = "4G"
+ String memory = "4G"
+ String javaXmx = "3G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir scatter_list
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
IntervalListTools \
SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
@@ -641,8 +654,9 @@ task SortVcf {
String outputVcfPath
File? dict
- String memory = "24G"
+ String memory = "9G"
String javaXmx = "8G"
+ Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -650,7 +664,7 @@ task SortVcf {
command {
set -e
mkdir -p "$(dirname ~{outputVcfPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
SortVcf \
I=~{sep=" I=" vcfFiles} \
~{"SEQUENCE_DICTIONARY=" + dict} \
@@ -664,6 +678,7 @@ task SortVcf {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -676,6 +691,7 @@ task SortVcf {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -686,15 +702,16 @@ task RenameSample {
File inputVcf
String outputPath = "./picard/renamed.vcf"
String newSampleName
- String memory = "24G"
+ String memory = "9G"
String javaXmx = "8G"
+ Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- picard -Xmx~{javaXmx} \
+ picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
RenameSampleInVcf \
I=~{inputVcf} \
O=~{outputPath} \
@@ -707,6 +724,7 @@ task RenameSample {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -717,6 +735,7 @@ task RenameSample {
newSampleName: {description: "A string to replace the old sample name.", category: "required"}
memory: {description: "The memory required to run the programs", category: "advanced"}
javaXmx: {description: "The max. memory allocated for JAVA", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
diff --git a/rtg.wdl b/rtg.wdl
index 8fd53ca4a4324b388c6f18c1c0584a26d013fe66..104a5ef9f29811ffde4d81a3b96da77d5bf728fc 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -27,7 +27,8 @@ task Format {
Array[File]+ inputFiles
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
String rtgMem = "8G"
- String memory = "16G"
+ String memory = "9G"
+ Int timeMinutes = 1 + ceil(size(inputFiles) * 2)
}
command {
@@ -45,15 +46,17 @@ task Format {
runtime {
docker: dockerImage
memory: memory
+ time_minutes: timeMinutes
}
parameter_meta {
- format: {description: "Format of input. Allowed values are [fasta, fastq, fastq-interleaved, sam-se, sam-pe] (Default is fasta)",
+ format: {description: "Format of input. Allowed values are [fasta, fastq, fastq-interleaved, sam-se, sam-pe].",
category: "advanced"}
outputPath: {description: "Where the output should be placed.", category: "advanced"}
inputFiles: {description: "input sequence files. May be specified 1 or more times.", category: "required"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
rtgMem: {description: "The amount of memory rtg will allocate to the JVM", category: "advanced"}
}
@@ -77,7 +80,8 @@ task VcfEval {
String outputMode = "split"
Int threads = 1 # tool default is number of cores in the system 😱
String rtgMem = "8G"
- String memory = "16G"
+ String memory = "9G"
+ Int timeMinutes = 1 + ceil(size([baseline, calls], "G") * 5)
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
}
@@ -131,6 +135,7 @@ task VcfEval {
docker: dockerImage
cpu: threads
memory: memory
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -157,6 +162,7 @@ task VcfEval {
threads: {description: "Number of threads. Default is 1", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
rtgMem: {description: "The amount of memory rtg will allocate to the JVM", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
}
diff --git a/samtools.wdl b/samtools.wdl
index 5521c6aaa5f93badddc571acf400f52afa98de1f..5648eb1cf403fbe3c877fe72f3cae066514d7026 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -26,6 +26,7 @@ task BgzipAndIndex {
String outputDir
String type = "vcf"
+ Int timeMinutes = 1 + ceil(size(inputFile, "G"))
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
}
@@ -44,7 +45,8 @@ task BgzipAndIndex {
}
runtime {
- docker: dockerImage
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -52,6 +54,7 @@ task BgzipAndIndex {
inputFile: {description: "The file to be compressed and indexed.", category: "required"}
outputDir: {description: "The directory in which the output will be placed.", category: "required"}
type: {description: "The type of file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -95,131 +98,195 @@ task Faidx {
}
}
-task Index {
+task Fastq {
input {
- File bamFile
- String? outputBamPath
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputRead0
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Boolean appendReadNumber = false
+ Boolean outputQuality = false
+ Int? compressionLevel
+
+ Int threads = 1
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(inputBam) * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- # Select_first is needed, otherwise womtool validate fails.
- String outputPath = select_first([outputBamPath, basename(bamFile)])
- String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
-
command {
- bash -c '
- set -e
- # Make sure outputBamPath does not exist.
- if [ ! -f ~{outputPath} ]
- then
- mkdir -p "$(dirname ~{outputPath})"
- ln ~{bamFile} ~{outputPath}
- fi
- samtools index ~{outputPath} ~{bamIndexPath}
- '
+ samtools fastq \
+ ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
+ ~{"-2 " + outputRead2} \
+ ~{"-0 " + outputRead0} \
+ ~{"-f " + includeFilter} \
+ ~{"-F " + excludeFilter} \
+ ~{"-G " + excludeSpecificFilter} \
+ ~{true="-N" false="-n" appendReadNumber} \
+ ~{true="-O" false="" outputQuality} \
+ ~{"-c " + compressionLevel} \
+ ~{"--threads " + threads} \
+ ~{inputBam}
}
output {
- File indexedBam = outputPath
- File index = bamIndexPath
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? read0 = outputRead0
}
runtime {
+ cpu: threads
+ memory: memory
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
- bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
- outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
- category: "common"}
+ inputBam: {description: "The bam file to process.", category: "required"}
+ outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
+ outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
+ outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
+ includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`", category: "advanced"}
+ excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`", category: "advanced"}
+ excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`", category: "advanced"}
+ appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`", category: "advanced"}
+ outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
-task Merge {
+task FilterShortReadsBam {
input {
- Array[File]+ bamFiles
- String outputBamPath = "merged.bam"
- Boolean force = true
-
+ File bamFile
+ String outputPathBam
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- String indexPath = sub(outputBamPath, "\.bam$",".bai")
+
+ String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
command {
set -e
- mkdir -p "$(dirname ~{outputBamPath})"
- samtools merge ~{true="-f" false="" force} ~{outputBamPath} ~{sep=' ' bamFiles}
- samtools index ~{outputBamPath} ~{indexPath}
+ mkdir -p "$(dirname ~{outputPathBam})"
+ samtools view -h ~{bamFile} | \
+ awk 'length($10) > 30 || $1 ~/^@/' | \
+ samtools view -bS -> ~{outputPathBam}
+ samtools index ~{outputPathBam} ~{outputPathBamIndex}
}
output {
- File outputBam = outputBamPath
- File outputBamIndex = indexPath
+ File filteredBam = outputPathBam
+ File filteredBamIndex = outputPathBamIndex
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- # inputs
- bamFiles: {description: "The BAM files to merge.", category: "required"}
- outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
- force: {description: "Equivalent to samtools merge's `-f` flag.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ bamFile: {description: "The bam file to process.", category: "required"}
+ outputPathBam: {description: "The filtered bam file.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
-task Sort {
+task Flagstat {
input {
File inputBam
String outputPath
- Boolean sortByName = false
- Int compressionLevel = 1
-
- String memory = "2G"
- String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
- Int? threads
+ String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G"))
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- samtools sort \
- -l ~{compressionLevel} \
- ~{true="-n" false="" sortByName} \
- ~{"--threads " + threads} \
- -o ~{outputPath} \
- ~{inputBam}
+ samtools flagstat ~{inputBam} > ~{outputPath}
}
output {
- File outputSortedBam = outputPath
+ File flagstat = outputPath
}
runtime {
- cpu: 1 + select_first([threads, 0])
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
- inputBam: {description: "The input SAM file.", category: "required"}
- outputPath: {description: "Output directory path + output file.", category: "required"}
- sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
- compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- memory: {description: "The amount of memory available to the job.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+ inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
+ outputPath: {description: "The location the ouput should be written to.", category: "required"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
- # outputs
- outputSortedBam: {description: "Sorted BAM file."}
+task Index {
+ input {
+ File bamFile
+ String? outputBamPath
+ String memory = "2G"
+ Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
+ }
+
+ # Select_first is needed, otherwise womtool validate fails.
+ String outputPath = select_first([outputBamPath, basename(bamFile)])
+ String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
+
+ command {
+ bash -c '
+ set -e
+ # Make sure outputBamPath does not exist.
+ if [ ! -f ~{outputPath} ]
+ then
+ mkdir -p "$(dirname ~{outputPath})"
+ ln ~{bamFile} ~{outputPath}
+ fi
+ samtools index ~{outputPath} ~{bamIndexPath}
+ '
+ }
+
+ output {
+ File indexedBam = outputPath
+ File index = bamIndexPath
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
+ outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
+ category: "common"}
+ memory: {description: "The amount of memory needed for the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
@@ -228,6 +295,7 @@ task Markdup {
File inputBam
String outputBamPath
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
@@ -243,108 +311,105 @@ task Markdup {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
inputBam: {description: "The BAM file to be processed.", category: "required"}
outputBamPath: {description: "The location of the output BAM file.", category: "required"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
-task Flagstat {
+task Merge {
input {
- File inputBam
- String outputPath
+ Array[File]+ bamFiles
+ String outputBamPath = "merged.bam"
+ Boolean force = true
+ Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
+ String indexPath = sub(outputBamPath, "\.bam$",".bai")
command {
set -e
- mkdir -p "$(dirname ~{outputPath})"
- samtools flagstat ~{inputBam} > ~{outputPath}
+ mkdir -p "$(dirname ~{outputBamPath})"
+ samtools merge ~{true="-f" false="" force} ~{outputBamPath} ~{sep=' ' bamFiles}
+ samtools index ~{outputBamPath} ~{indexPath}
}
output {
- File flagstat = outputPath
+ File outputBam = outputBamPath
+ File outputBamIndex = indexPath
}
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
- inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
- outputPath: {description: "The location the ouput should be written to.", category: "required"}
+ bamFiles: {description: "The BAM files to merge.", category: "required"}
+ outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
+ force: {description: "Equivalent to samtools merge's `-f` flag.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
-task Fastq {
+task Sort {
input {
File inputBam
- String outputRead1
- String? outputRead2
- String? outputRead0
- Int? includeFilter
- Int? excludeFilter
- Int? excludeSpecificFilter
- Boolean appendReadNumber = false
- Boolean outputQuality = false
- Int? compressionLevel
+ String outputPath
+ Boolean sortByName = false
+ Int compressionLevel = 1
- Int threads = 1
- String memory = "1G"
- String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
+ String memory = "2G"
+ String dockerImage = "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
+ Int? threads
}
command {
- samtools fastq \
- ~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
- ~{"-2 " + outputRead2} \
- ~{"-0 " + outputRead0} \
- ~{"-f " + includeFilter} \
- ~{"-F " + excludeFilter} \
- ~{"-G " + excludeSpecificFilter} \
- ~{true="-N" false="-n" appendReadNumber} \
- ~{true="-O" false="" outputQuality} \
- ~{"-c " + compressionLevel} \
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ samtools sort \
+ -l ~{compressionLevel} \
+ ~{true="-n" false="" sortByName} \
~{"--threads " + threads} \
+ -o ~{outputPath} \
~{inputBam}
}
output {
- File read1 = outputRead1
- File? read2 = outputRead2
- File? read0 = outputRead0
+ File outputSortedBam = outputPath
}
runtime {
- cpu: threads
+ cpu: 1 + select_first([threads, 0])
memory: memory
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
# inputs
- inputBam: {description: "The bam file to process.", category: "required"}
- outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
- outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
- outputRead0: {description: "The location the unpaired reads should be written to (in case of paired-end sequenicng).", category: "advanced"}
- includeFilter: {description: "Include reads with ALL of these flags. Corresponds to `-f`", category: "advanced"}
- excludeFilter: {description: "Exclude reads with ONE OR MORE of these flags. Corresponds to `-F`", category: "advanced"}
- excludeSpecificFilter: {description: "Exclude reads with ALL of these flags. Corresponds to `-G`", category: "advanced"}
- appendReadNumber: {description: "Append /1 and /2 to the read name, or don't. Corresponds to `-n/N`", category: "advanced"}
- outputQuality: {description: "Equivalent to samtools fastq's `-O` flag.", category: "advanced"}
- threads: {description: "The number of threads to use.", category: "advanced"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ inputBam: {description: "The input SAM file.", category: "required"}
+ outputPath: {description: "Output directory path + output file.", category: "required"}
+ sortByName: {description: "Sort the inputBam by read name instead of position.", category: "advanced"}
+ compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ # outputs
+ outputSortedBam: {description: "Sorted BAM file."}
}
}
@@ -353,6 +418,7 @@ task Tabix {
File inputFile
String outputFilePath = "indexed.vcf.gz"
String type = "vcf"
+ Int timeMinutes = 1 + ceil(size(inputFile, "G") * 2)
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
}
# FIXME: It is better to do the indexing on VCF creation. Not in a separate task. With file localization this gets hairy fast.
@@ -372,6 +438,7 @@ task Tabix {
}
runtime {
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -381,6 +448,7 @@ task Tabix {
outputFilePath: {description: "The location where the file should be written to. The index will appear alongside this link to the file.",
category: "common"}
type: {description: "The type of file (eg. vcf or bed) to be indexed.", category: "common"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -399,6 +467,7 @@ task View {
Int threads = 1
String memory = "1G"
+ Int timeMinutes = 1 + ceil(size(inFile, "G") * 5)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
String outputIndexPath = basename(outputFileName) + ".bai"
@@ -428,6 +497,7 @@ task View {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -444,41 +514,8 @@ task View {
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
-}
-
-task FilterShortReadsBam {
- input {
- File bamFile
- String outputPathBam
- String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
- }
-
- String outputPathBamIndex = sub(outputPathBam, "\.bam$", ".bai")
-
- command {
- set -e
- mkdir -p "$(dirname ~{outputPathBam})"
- samtools view -h ~{bamFile} | \
- awk 'length($10) > 30 || $1 ~/^@/' | \
- samtools view -bS -> ~{outputPathBam}
- samtools index ~{outputPathBam} ~{outputPathBamIndex}
- }
-
- output {
- File filteredBam = outputPathBam
- File filteredBamIndex = outputPathBamIndex
- }
-
- runtime {
- docker: dockerImage
- }
-
- parameter_meta {
- bamFile: {description: "The bam file to process.", category: "required"}
- outputPathBam: {description: "The filtered bam file.", category: "common"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- }
-}
+}
\ No newline at end of file
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 49e5c36d4a5b388e596bcd2c943812f8011c3a57..7b9a4403c6e31c1ad6374b4561bfaee96dc4c435 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -47,6 +47,7 @@ task ParallelPaired {
File? strelkaIndel
Int threads = 1
+ Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
@@ -89,6 +90,7 @@ task ParallelPaired {
runtime {
cpu: threads
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -118,6 +120,7 @@ task ParallelPaired {
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -150,6 +153,7 @@ task ParallelPairedTrain {
File? strelkaIndel
Int threads = 1
+ Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
@@ -191,6 +195,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -220,6 +225,7 @@ task ParallelPairedTrain {
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -244,6 +250,7 @@ task ParallelSingle {
File? strelkaVCF
Int threads = 1
+ Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
@@ -279,6 +286,7 @@ task ParallelSingle {
runtime {
cpu: threads
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -300,6 +308,7 @@ task ParallelSingle {
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -324,6 +333,7 @@ task ParallelSingleTrain {
File? strelkaVCF
Int threads = 1
+ Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
@@ -358,6 +368,7 @@ task ParallelSingleTrain {
runtime {
cpu: threads
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -379,6 +390,7 @@ task ParallelSingleTrain {
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -389,6 +401,7 @@ task ModifyStrelka {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
String dockerImage = "lethalfang/somaticseq:3.1.0"
+ Int timeMinutes = 20
}
command {
@@ -407,12 +420,14 @@ task ModifyStrelka {
}
runtime {
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
strelkaVCF: {description: "A vcf file as produced by strelka.", category: "required"}
outputVCFName: {description: "The location the output VCF file should be written to.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/star.wdl b/star.wdl
index 5d0d6b6c2999c53b65bf7c66ed31ac1d5ae7f31b..4942f35e167a4ff14d272b3911e8bd4d68904914 100644
--- a/star.wdl
+++ b/star.wdl
@@ -89,7 +89,7 @@ task GenomeGenerate {
task Star {
input {
Array[File]+ inputR1
- Array[File]? inputR2
+ Array[File] inputR2 = []
Array[File]+ indexFiles
String outFileNamePrefix
String outSAMtype = "BAM SortedByCoordinate"
@@ -101,7 +101,8 @@ task Star {
Int? limitBAMsortRAM
Int runThreadN = 4
- String memory = "48G"
+ String memory = "~{5 + ceil(size(indexFiles, "G"))}G"
+ Int timeMinutes = 1 + ceil(size(flatten([inputR1, inputR2]), "G") * 180 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
@@ -133,6 +134,7 @@ task Star {
runtime {
cpu: runThreadN
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -150,6 +152,7 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/strelka.wdl b/strelka.wdl
index 826cbd8e260014c1816d6640c313f3ebbb39bdef..50c38b55ae4374efc7ea32e7be8f6e08a0076cdb 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -36,6 +36,7 @@ task Germline {
Int cores = 1
Int memoryGb = 4
+ Int timeMinutes = 90
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
}
@@ -62,6 +63,7 @@ task Germline {
runtime {
docker: dockerImage
cpu: cores
+ time_minutes: timeMinutes
memory: "~{memoryGb}G"
}
@@ -78,6 +80,7 @@ task Germline {
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -100,6 +103,7 @@ task Somatic {
Int cores = 1
Int memoryGb = 4
+ Int timeMinutes = 90
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
File? doNotDefineThis #FIXME
@@ -131,6 +135,7 @@ task Somatic {
runtime {
docker: dockerImage
cpu: cores
+ time_minutes: timeMinutes
memory: "~{memoryGb}G"
}
@@ -150,6 +155,7 @@ task Somatic {
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/stringtie.wdl b/stringtie.wdl
index cfaccc92f80d1ab9d489e37e31ea2dd3e28c0584..5ed62deadd8758f2b476b3ff02cf79fb9d1a719a 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -32,7 +32,8 @@ task Stringtie {
String? geneAbundanceFile
Int threads = 1
- String memory = "10G"
+ String memory = "2G"
+ Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
@@ -58,54 +59,24 @@ task Stringtie {
runtime {
cpu: threads
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- bam: {
- description: "The input BAM file.",
- category: "required"
- }
- bamIndex: {
- description: "The input BAM file's index.",
- category: "required"
- }
- referenceGtf: {
- description: "A reference GTF file to be used as guide.",
- category: "common"
- }
- skipNovelTranscripts: {
- description: "Whether new transcripts should be assembled or not.",
- category: "common"
- }
- assembledTranscriptsFile: {
- description: "Where the output of the assembly should be written.",
- category: "required"
- }
- firstStranded: {
- description: "Equivalent to the --rf flag of stringtie.",
- category: "required"
- }
- secondStranded: {
- description: "Equivalent to the --fr flag of stringtie.",
- category: "required"
- }
- geneAbundanceFile: {
- description: "Where the abundance file should be written.",
- category: "common"
- }
- threads: {
- description: "The number of threads to use.",
- category: "advanced"
- }
- memory: {
- description: "The amount of memory needed for this task in GB.",
- category: "advanced"
- }
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ bam: {description: "The input BAM file.", category: "required"}
+ bamIndex: {description: "The input BAM file's index.", category: "required"}
+ referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
+ skipNovelTranscripts: {description: "Whether new transcripts should be assembled or not.", category: "common"}
+ assembledTranscriptsFile: {description: "Where the output of the assembly should be written.", category: "required"}
+ firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
+ secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
+ geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
@@ -123,6 +94,7 @@ task Merge {
String? label
String memory = "10G"
+ Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
@@ -148,57 +120,24 @@ task Merge {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
- gtfFiles: {
- description: "The GTF files produced by stringtie.",
- category: "required"
- }
- outputGtfPath: {
- description: "Where the output should be written.",
- category: "required"
- }
- guideGtf: {
- description: "Equivalent to the -G option of 'stringtie --merge'.",
- category: "advanced"
- }
- minimumLength: {
- description: "Equivalent to the -m option of 'stringtie --merge'.",
- category: "advanced"
- }
- minimumCoverage: {
- description: "Equivalent to the -c option of 'stringtie --merge'.",
- category: "advanced"
- }
- minimumFPKM: {
- description: "Equivalent to the -F option of 'stringtie --merge'.",
- category: "advanced"
- }
- minimumTPM: {
- description: "Equivalent to the -T option of 'stringtie --merge'.",
- category: "advanced"
- }
- minimumIsoformFraction: {
- description: "Equivalent to the -f option of 'stringtie --merge'.",
- category: "advanced"
- }
- keepMergedTranscriptsWithRetainedIntrons: {
- description: "Equivalent to the -i flag of 'stringtie --merge'.",
- category: "advanced"
- }
- label: {
- description: "Equivalent to the -l option of 'stringtie --merge'.",
- category: "advanced"
- }
- memory: {
- description: "The amount of memory needed for this task in GB.",
- category: "advanced"
- }
- dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"
- }
+ gtfFiles: {description: "The GTF files produced by stringtie.", category: "required"}
+ outputGtfPath: {description: "Where the output should be written.", category: "required"}
+ guideGtf: {description: "Equivalent to the -G option of 'stringtie --merge'.", category: "advanced"}
+ minimumLength: {description: "Equivalent to the -m option of 'stringtie --merge'.", category: "advanced"}
+ minimumCoverage: {description: "Equivalent to the -c option of 'stringtie --merge'.", category: "advanced"}
+ minimumFPKM: {description: "Equivalent to the -F option of 'stringtie --merge'.", category: "advanced"}
+ minimumTPM: {description: "Equivalent to the -T option of 'stringtie --merge'.", category: "advanced"}
+ minimumIsoformFraction: {description: "Equivalent to the -f option of 'stringtie --merge'.", category: "advanced"}
+ keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
+ label: {description: "Equivalent to the -l option of 'stringtie --merge'.", category: "advanced"}
+ memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
}
}
diff --git a/survivor.wdl b/survivor.wdl
index ded11d75a64b9de98312a520d0fd284aa0ecda5c..e5ac7b5bfb3bf8b2a9230f6c65f790287a4bafb8 100644
--- a/survivor.wdl
+++ b/survivor.wdl
@@ -33,6 +33,7 @@ task Merge {
Int minSize = 30
String outputPath = "./survivor/merged.vcf"
String memory = "24G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
}
@@ -57,6 +58,7 @@ task Merge {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -71,6 +73,7 @@ task Merge {
minSize: {description: "The mimimum size of SV to be merged", category: "advanced"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
diff --git a/talon.wdl b/talon.wdl
index 6ddb841e12a76a99ba2b94f776f91c3315f8de38..b2ae3a622067184bfb6fc5524cdd7b137460d10e 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -31,6 +31,7 @@ task CreateAbundanceFileFromDatabase {
File? datasetsFile
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -52,6 +53,7 @@ task CreateAbundanceFileFromDatabase {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -64,6 +66,7 @@ task CreateAbundanceFileFromDatabase {
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetsFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -84,6 +87,7 @@ task CreateGtfFromDatabase {
File? datasetFile
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -106,6 +110,7 @@ task CreateGtfFromDatabase {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -119,6 +124,7 @@ task CreateGtfFromDatabase {
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -135,6 +141,7 @@ task FilterTalonTranscripts {
File? pairingsFile
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -154,6 +161,7 @@ task FilterTalonTranscripts {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -164,6 +172,7 @@ task FilterTalonTranscripts {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
pairingsFile: {description: "A file indicating which datasets should be considered together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -180,6 +189,7 @@ task GetReadAnnotations {
File? datasetFile
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -199,6 +209,7 @@ task GetReadAnnotations {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -209,6 +220,7 @@ task GetReadAnnotations {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -228,6 +240,7 @@ task InitializeTalonDatabase {
String outputPrefix
String memory = "10G"
+ Int timeMinutes = 60
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -251,6 +264,7 @@ task InitializeTalonDatabase {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -265,6 +279,7 @@ task InitializeTalonDatabase {
cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -277,6 +292,7 @@ task ReformatGtf {
File GTFfile
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -292,6 +308,7 @@ task ReformatGtf {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -299,6 +316,7 @@ task ReformatGtf {
# inputs
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -315,6 +333,7 @@ task SummarizeDatasets {
File? datasetGroupsCSV
String memory = "4G"
+ Int timeMinutes = 50
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -334,6 +353,7 @@ task SummarizeDatasets {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -344,6 +364,7 @@ task SummarizeDatasets {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
@@ -364,6 +385,7 @@ task Talon {
Int cores = 4
String memory = "25G"
+ Int timeMinutes = 2880
String dockerImage = "biocontainers/talon:v4.4.2_cv1"
}
@@ -399,6 +421,7 @@ task Talon {
runtime {
cpu: cores
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -414,6 +437,7 @@ task Talon {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index 68bcbf240ca1f5845c0848ca07b477986794b611..15da1f583ee7c0271e3e54751d2c588cbba5087d 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -28,6 +28,7 @@ task GetSJsFromGtf {
Int minIntronSize = 21
String memory = "8G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -47,6 +48,7 @@ task GetSJsFromGtf {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -57,6 +59,7 @@ task GetSJsFromGtf {
minIntronSize: {description: "Minimum size of intron to consider a junction.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
@@ -70,6 +73,7 @@ task GetTranscriptCleanStats {
String outputPrefix
String memory = "4G"
+ Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -87,6 +91,7 @@ task GetTranscriptCleanStats {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -95,6 +100,7 @@ task GetTranscriptCleanStats {
transcriptCleanSAMfile: {description: "Output SAM file from TranscriptClean", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
@@ -124,6 +130,7 @@ task TranscriptClean {
Int cores = 1
String memory = "25G"
+ Int timeMinutes = 2880
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
@@ -159,6 +166,7 @@ task TranscriptClean {
runtime {
cpu: cores
memory: memory
+ time_minute: timeMinutes
docker: dockerImage
}
@@ -181,6 +189,7 @@ task TranscriptClean {
variantFile: {description: "VCF formatted file of variants.", category: "common"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
diff --git a/umi-tools.wdl b/umi-tools.wdl
index 07518e57e5954077f643645d5f43ad03f09611ea..c5f3b145c50c30465652c29c96523a0b4687bf81 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -29,7 +29,7 @@ task Extract {
Boolean threePrime = false
String read1Output = "umi_extracted_R1.fastq.gz"
String? read2Output = "umi_extracted_R2.fastq.gz"
-
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
}
@@ -51,6 +51,7 @@ task Extract {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
}
parameter_meta {
@@ -61,6 +62,7 @@ task Extract {
threePrime: {description: "Whether or not the UMI's are at the reads' 3' end. If false the UMIs are extracted from the 5' end.", category: "advanced"}
read1Output: {description: "The location to write the first/single-end output fastq file to.", category: "advanced"}
read2Output: {description: "The location to write the second-end output fastq file to.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -75,7 +77,8 @@ task Dedup {
String? statsPrefix
Boolean paired = true
- String memory = "5G"
+ String memory = "25G"
+ Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
@@ -105,6 +108,7 @@ task Dedup {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -116,6 +120,7 @@ task Dedup {
umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
paired: {description: "Whether or not the data is paired.", category: "common"}
memory: {description: "The amount of memory required for the task.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/vardict.wdl b/vardict.wdl
index 7bfd118ee99f67da1af482b240d1f9c6d34fe9f1..92beb32e91ec14baf170183b9bdc283f83850595 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -48,14 +48,15 @@ task VarDict {
Float minimumAlleleFrequency = 0.02
Int threads = 1
- String memory = "40G"
+ String memory = "18G"
String javaXmx = "16G"
+ Int timeMinutes = 300
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
}
command {
set -e -o pipefail
- export JAVA_OPTS="-Xmx~{javaXmx}"
+ export JAVA_OPTS="-Xmx~{javaXmx} -XX:ParallelGCThreads=1"
vardict-java \
~{"-th " + threads} \
-G ~{referenceFasta} \
@@ -87,6 +88,7 @@ task VarDict {
runtime {
cpu: threads + 2
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -116,6 +118,7 @@ task VarDict {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/vt.wdl b/vt.wdl
index 54599db01b78b900c172516993d3e6399f036f6b..d4c134b98ffa2e0e30910a4c1241b1e11df467f8 100644
--- a/vt.wdl
+++ b/vt.wdl
@@ -29,6 +29,7 @@ task Normalize {
String outputPath = "./vt/normalized_decomposed.vcf"
String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
String memory = "4G"
+ Int timeMinutes = 30
}
command {
@@ -43,6 +44,7 @@ task Normalize {
runtime {
memory: memory
+ time_minutes: timeMinutes
docker: dockerImage
}
@@ -54,6 +56,7 @@ task Normalize {
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}