From 163290340ff4f5ed0488c69d2c194dbb3428a423 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 2 Nov 2020 11:57:06 +0100
Subject: [PATCH] Add another batch of updated tasks.
---
CHANGELOG.md | 4 +
centrifuge.wdl | 4 +-
ncbi.wdl | 51 ++++----
pbbam.wdl | 10 +-
pbmm2.wdl | 13 ++-
picard.wdl | 312 +++++++++++++++++++++++--------------------------
rtg.wdl | 79 ++++++-------
sambamba.wdl | 57 +++++----
8 files changed, 257 insertions(+), 273 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c331112..f0dfaf1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,10 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Picard: Add parameter_meta to `SortSam`.
++ pbmm2: Add parameter_meta for `sample`.
++ Centrifuge: Rename output in task `KReport` to `KrakenReport` to resolve
+ name collision with task name.
+ Bwa & bwa-mem2: Add parameter_meta for `outputHla`.
+ Multiqc: Removed WDL_AID excludes of "finished" & "dependencies" inputs.
+ Bam2fastx: Add localisation of input files to Bam2Fasta task.
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 1637abd..07dc7f8 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -270,7 +270,7 @@ task KReport {
>>>
output {
- File KReport = outputPrefix + "_kreport.tsv"
+ File KrakenReport = outputPrefix + "_kreport.tsv"
}
runtime {
@@ -294,7 +294,7 @@ task KReport {
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
- KReport: {description: "File with kraken style report."}
+ KrakenReport: {description: "File with kraken style report."}
}
}
diff --git a/ncbi.wdl b/ncbi.wdl
index d157d90..da753ba 100644
--- a/ncbi.wdl
+++ b/ncbi.wdl
@@ -23,6 +23,10 @@ version 1.0
task GenomeDownload {
input {
String outputPath
+ Boolean verbose = true
+ Boolean debug = false
+ String executable = "ncbi-genome-download"
+
String? section = "refseq"
String? format = "all"
String? assemblyLevel = "all"
@@ -32,11 +36,7 @@ task GenomeDownload {
String? ncbiBaseUri
Int? parallel
Int? retries
- Boolean verbose = true
- Boolean debug = false
String? domain = "all"
-
- String executable = "ncbi-genome-download"
String? preCommand
}
@@ -58,22 +58,22 @@ task GenomeDownload {
~{true="--debug" false ="" debug } \
~{domain}
- # Check md5sums for all downloaded files
+ # Check md5sums for all downloaded files.
for folder in $(realpath ~{outputPath})/*/*/*
- do
- (
- md5sums="$(
- cd $folder
- for file in *
- do
- if [[ ! $file == "MD5SUMS" ]]
- then
- grep $file MD5SUMS
- fi
- done
- )"
- cd $folder; echo $md5sums | md5sum -c)
- done
+ do
+ (
+ md5sums="$(
+ cd $folder
+ for file in *
+ do
+ if [[ ! $file == "MD5SUMS" ]]
+ then
+ grep $file MD5SUMS
+ fi
+ done
+ )"
+ cd $folder; echo $md5sums | md5sum -c)
+ done
}
output {
@@ -106,7 +106,7 @@ task DownloadNtFasta{
mkdir -p ~{ntDir}
rsync -av --partial rsync://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz* ~{ntDir}
(cd ~{ntDir} && md5sum -c nt.gz.md5)
- # Only unzip when necessary
+ # Only unzip when necessary.
if ~{true='true' false='false' unzip}
then
zcat ~{ntDir}/nt.gz > ~{ntFilePath}
@@ -132,15 +132,16 @@ task DownloadAccessionToTaxId {
command {
set -e -o pipefail
mkdir -p ~{downloadDir}
- rsync -av \
- --partial \
- rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* \
- ~{downloadDir}
+ rsync \
+ -av \
+ --partial \
+ rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* \
+ ~{downloadDir}
(cd ~{downloadDir} && md5sum -c *.md5)
for file in ~{downloadDir}/nucl_*.accession2taxid.gz
do
zcat $file | tail -n +2 | cut -f 2,3 ~{true="| gzip" false='' gzip} > \
- $file.seqtaxmap~{true='.gz' false='' gzip}
+ $file.seqtaxmap~{true='.gz' false='' gzip}
done
}
diff --git a/pbbam.wdl b/pbbam.wdl
index 52737a0..d271a11 100644
--- a/pbbam.wdl
+++ b/pbbam.wdl
@@ -18,12 +18,14 @@ version 1.0
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
task Index {
input {
File bamFile
+
String? outputBamPath
-
+
String memory = "2G"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
String dockerImage = "quay.io/biocontainers/pbbam:1.6.0--h5b7e6e0_0"
@@ -60,11 +62,9 @@ task Index {
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"}
+ 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"}
+ 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/pbmm2.wdl b/pbmm2.wdl
index 31d4c66..5fda1c8 100644
--- a/pbmm2.wdl
+++ b/pbmm2.wdl
@@ -8,10 +8,10 @@ version 1.0
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -58,9 +58,10 @@ task Mapping {
}
parameter_meta {
+ # inputs
presetOption: {description: "This option applies multiple options at the same time.", category: "required"}
sort: {description: "Sort the output bam file.", category: "advanced"}
- sample: {description: "Name of the sample"}
+ sample: {description: "Name of the sample.", category: "required"}
referenceMMI: {description: "MMI file for the reference.", category: "required"}
queryFile: {description: "BAM file with reads to align against the reference.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
@@ -68,7 +69,7 @@ task Mapping {
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
+ # outputs
outputAlignmentFile: {description: "Mapped bam file."}
outputIndexFile: {description: "Bam index file."}
}
diff --git a/picard.wdl b/picard.wdl
index 49db8b8..f1876f7 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -26,8 +26,8 @@ task BedToIntervalList {
File dict
String outputPath = "regions.interval_list"
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4G"
Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -47,9 +47,9 @@ task BedToIntervalList {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -57,12 +57,10 @@ task BedToIntervalList {
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"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
@@ -74,17 +72,19 @@ task CollectHsMetrics {
File referenceFastaDict
File referenceFastaFai
File targets
- File? baits
String basename
+ File? baits
+
# Use the targets file as baits as a fallback, since often the baits
# for a certain capture kit are not available.
File baitsFile = select_first([baits, targets])
File targetsFile = targets
- Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 3072
- # Additional * 2 because picard multiple metrics reads the reference fasta twice.
+ Int memoryMb = javaXmxMb + 512
+ # Additional * 2 because picard multiple metrics reads the
+ # reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -106,9 +106,9 @@ task CollectHsMetrics {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -116,18 +116,15 @@ task CollectHsMetrics {
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"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- 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"}
targets: {description: "Picard interval file of the capture targets.", category: "required"}
- baits: {description: "Picard interval file of the capture bait set.", category: "advanced"}
basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
+ baits: {description: "Picard interval file of the capture bait set.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` 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"}
+ 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"}
}
}
@@ -139,7 +136,6 @@ task CollectMultipleMetrics {
File referenceFastaDict
File referenceFastaFai
String basename
-
Boolean collectAlignmentSummaryMetrics = true
Boolean collectInsertSizeMetrics = true
Boolean qualityScoreDistribution = true
@@ -150,14 +146,13 @@ task CollectMultipleMetrics {
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
- Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 3072
+ Int memoryMb = javaXmxMb + 512
# Additional * 2 because picard multiple metrics reads the reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
-
command {
set -e
mkdir -p "$(dirname ~{basename})"
@@ -173,8 +168,7 @@ task CollectMultipleMetrics {
~{true="PROGRAM=MeanQualityByCycle" false="" meanQualityByCycle} \
~{true="PROGRAM=CollectBaseDistributionByCycle" false="" collectBaseDistributionByCycle} \
~{true="PROGRAM=CollectGcBiasMetrics" false="" collectGcBiasMetrics} \
- ~{true="PROGRAM=CollectSequencingArtifactMetrics" false=""
- collectSequencingArtifactMetrics} \
+ ~{true="PROGRAM=CollectSequencingArtifactMetrics" false="" collectSequencingArtifactMetrics} \
~{true="PROGRAM=CollectQualityYieldMetrics" false="" collectQualityYieldMetrics}
}
@@ -221,9 +215,9 @@ task CollectMultipleMetrics {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -231,30 +225,21 @@ task CollectMultipleMetrics {
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"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- 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"}
- 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"}
+ 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"}
- collectBaseDistributionByCycle: {description: "Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.",
- category: "advanced"}
+ collectBaseDistributionByCycle: {description: "Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` 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.",
- category: "advanced"}
+ collectSequencingArtifactMetrics: {description: "Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.", category: "advanced"}
+ collectQualityYieldMetrics: {description: "Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` 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"}
+ 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"}
}
}
@@ -266,9 +251,9 @@ task CollectRnaSeqMetrics {
String basename
String strandSpecificity = "NONE"
- String memory = "9G"
String javaXmx = "8G"
- # With 6 minutes per G there were several timeouts.
+ String memory = "9G"
+ # With 6 minutes per G there were several timeouts.
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 12)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -286,14 +271,14 @@ task CollectRnaSeqMetrics {
}
output {
- File? chart = basename + ".RNA_Metrics.pdf"
File metrics = basename + ".RNA_Metrics"
+ File? chart = basename + ".RNA_Metrics.pdf"
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -302,15 +287,11 @@ task CollectRnaSeqMetrics {
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"}
- strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics.",
- category: "common"}
-
+ strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics.", category: "common"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
@@ -325,8 +306,8 @@ task CollectTargetedPcrMetrics {
Array[File]+ targetIntervals
String basename
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4G"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -352,9 +333,9 @@ task CollectTargetedPcrMetrics {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -362,21 +343,15 @@ task CollectTargetedPcrMetrics {
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"}
- referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
- 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"}
- ampliconIntervals: {description: "An interval list describinig the coordinates of the amplicons sequenced.",
- category: "required"}
- targetIntervals: {description: "An interval list describing the coordinates of the targets sequenced.",
- category: "required"}
+ ampliconIntervals: {description: "An interval list describinig the coordinates of the amplicons sequenced.", 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"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
@@ -388,8 +363,8 @@ task CollectVariantCallingMetrics {
File inputVCFIndex
String basename
- String memory = "9G"
String javaXmx = "8G"
+ String memory = "9G"
Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -410,24 +385,22 @@ task CollectVariantCallingMetrics {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
# inputs
dbsnp: {description: "DBSNP vcf file to use with CollectVariantCallingMetrics.", category: "required"}
dbsnpIndex: {description: "Index file for the DBSNP VCF.", category: "required"}
- inputVCF: {description: "Input VCF file", category: "required"}
+ inputVCF: {description: "Input VCF file.", category: "required"}
inputVCFIndex: {description: "Index file for the input VCF.", category: "required"}
basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
@@ -436,8 +409,8 @@ task CreateSequenceDictionary {
File inputFile
String outputDir
- String memory = "3G"
String javaXmx = "2G"
+ String memory = "3G"
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -464,8 +437,8 @@ task CreateSequenceDictionary {
# inputs
inputFile: {description: "The input fasta file.", category: "required"}
outputDir: {description: "Output directory path.", category: "required"}
- memory: {description: "The amount of memory available to the job.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
# outputs
@@ -473,17 +446,19 @@ task CreateSequenceDictionary {
}
}
-# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
+# Combine multiple recalibrated BAM files from scattered
+# ApplyRecalibration runs.
task GatherBamFiles {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
String outputBamPath
+ Boolean createMd5File = false
- Int memoryMb = javaXmxMb + 512
- Int javaXmxMb = 1024
Int? compressionLevel
- Boolean createMd5File = false
+
+ Int javaXmxMb = 1024
+ Int memoryMb = javaXmxMb + 512
# One minute per input gigabyte.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 1)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
@@ -508,9 +483,9 @@ task GatherBamFiles {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -518,14 +493,12 @@ task GatherBamFiles {
inputBams: {description: "The BAM files to be merged together.", category: "required"}
inputBamsIndex: {description: "The indexes of the input BAM files.", category: "required"}
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
- compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
createMd5File: {decription: "Whether to create an md5 file of the output BAM.", category: "advanced"}
+ compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` 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"}
+ 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"}
}
}
@@ -535,8 +508,8 @@ task GatherVcfs {
Array[File]+ inputVcfIndexes
String outputVcfPath = "out.vcf.gz"
- String memory = "5G"
String javaXmx = "4G"
+ String memory = "5G"
Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -555,9 +528,9 @@ task GatherVcfs {
}
runtime {
- docker: dockerImage
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -565,17 +538,14 @@ task GatherVcfs {
inputVcfs: {description: "The VCF files to be merged together.", category: "required"}
inputVcfIndexes: {description: "The indexes of the input VCF files.", category: "required"}
outputVcfPath: {description: "The path where the merged VCF file will be written.", caregory: "required"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
-# Mark duplicate reads to avoid counting non-independent observations
+# Mark duplicate reads to avoid counting non-independent observations.
task MarkDuplicates {
input {
Array[File]+ inputBams
@@ -583,31 +553,32 @@ task MarkDuplicates {
String metricsPath
Int compressionLevel = 1
Boolean createMd5File = false
- Boolean useJdkInflater = true # Slightly faster than the intel one.
- # Better results for compression level 1 (much smaller). Higher compression levels similar to intel deflater.
- # NOTE: this might change in the future when the intel deflater is updated!
+ Boolean useJdkInflater = true # Slightly faster than the intel one.
+ # Better results for compression level 1 (much smaller).
+ # Higher compression levels similar to intel deflater.
+ # NOTE: this might change in the future when the intel
+ # deflater is updated!
Boolean useJdkDeflater = true
- # In GATK Best practices pipeline MarkDuplicates is given a 7G VM.
+ # The program default for READ_NAME_REGEX is appropriate in nearly every case.
+ # Sometimes we wish to supply "null" in order to turn off optical duplicate detection.
+ # This can be desirable if you don't mind the estimated library size
+ # being wrong and optical duplicate detection is taking >7 days and failing.
+ String? read_name_regex
+
+ # In GATK Best practices pipeline MarkDuplicates is given a 7G VM.
# https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L1040
Int javaXmxMb = 6656 # 6.5G
String memoryMb = javaXmxMb + 512
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
-
- # The program default for READ_NAME_REGEX is appropriate in nearly every case.
- # Sometimes we wish to supply "null" in order to turn off optical duplicate detection
- # This can be desirable if you don't mind the estimated library size being wrong and
- # optical duplicate detection is taking >7 days and failing
- String? read_name_regex
}
# Task is assuming query-sorted input so that the Secondary and Supplementary reads get
# marked correctly. This works because the output of BWA is query-grouped and therefore,
# so is the output of MergeBamAlignment. While query-grouped isn't actually query-sorted,
- # it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname"
-
+ # it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname".
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
@@ -625,7 +596,7 @@ task MarkDuplicates {
ADD_PG_TAG_TO_READS=false \
CREATE_MD5_FILE=~{true="true" false="false" createMd5File} \
USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
- USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
}
output {
@@ -636,9 +607,9 @@ task MarkDuplicates {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: "~{memoryMb}M"
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -646,42 +617,39 @@ task MarkDuplicates {
inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
outputBamPath: {description: "The location where the ouptut BAM file should be written.", category: "required"}
metricsPath: {description: "The location where the output metrics file should be written.", category: "required"}
- read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
createMd5File: {description: "Whether to create a md5 file for the created BAM file.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
- compressionLevel: {description: "The compression level at which the BAM files are written", category: "advanced"}
+ read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
+ javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
- javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` 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"}
+ 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"}
}
}
-# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
+# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs.
task MergeVCFs {
input {
Array[File]+ inputVCFs
Array[File]+ inputVCFsIndexes
String outputVcfPath
-
- String memory = "5G"
- String javaXmx = "4G"
- Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
- String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
Int compressionLevel = 1
- Boolean useJdkInflater = true # Slightly faster than the intel one.
- # Better results for compression level 1 (much smaller). Higher compression levels similar to intel deflater.
+ Boolean useJdkInflater = true # Slightly faster than the intel one.
+ # Better results for compression level 1 (much smaller).
+ # Higher compression levels similar to intel deflater.
# NOTE: this might change in the future when the intel deflater is updated!
Boolean useJdkDeflater = true
+ String javaXmx = "4G"
+ String memory = "5G"
+ Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
+ String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
- # Using MergeVcfs instead of GatherVcfs so we can create indices
- # See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
-
+ # Using MergeVcfs instead of GatherVcfs so we can create indices.
+ # See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket.
command {
set -e
mkdir -p "$(dirname ~{outputVcfPath})"
@@ -691,7 +659,7 @@ task MergeVCFs {
OUTPUT=~{outputVcfPath} \
COMPRESSION_LEVEL=~{compressionLevel} \
USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
- USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
}
output {
@@ -700,9 +668,9 @@ task MergeVCFs {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -710,16 +678,13 @@ task MergeVCFs {
inputVCFs: {description: "The VCF files to be merged.", category: "required"}
inputVCFsIndexes: {description: "The indexes of the VCF files.", category: "required"}
outputVcfPath: {description: "The location the output VCF file should be written to.", 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"}
+ compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
- compressionLevel: {description: "The compression level at which the BAM files are written", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
}
}
@@ -729,10 +694,12 @@ task SamToFastq {
File inputBamIndex
Boolean paired = true
- String memory = "17G"
String javaXmx = "16G" # High memory default to avoid crashes.
+ String memory = "17G"
+ Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
- File? NONE
+
+ File? noneFile
}
String outputRead1 = basename(inputBam, "\.[bs]am") + "_R1.fastq.gz"
@@ -751,13 +718,20 @@ task SamToFastq {
output {
File read1 = outputRead1
- File? read2 = if paired then outputRead2 else NONE
- File? unpairedRead = if paired then outputUnpaired else NONE
+ File? read2 = if paired then outputRead2 else noneFile
+ File? unpairedRead = if paired then outputUnpaired else noneFile
}
runtime {
- docker: dockerImage
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ meta {
+ WDL_AID: {
+ exclude: ["noneFile"]
+ }
}
}
@@ -766,8 +740,8 @@ task ScatterIntervalList {
File interval_list
Int scatter_count
- String memory = "4G"
String javaXmx = "3G"
+ String memory = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
}
@@ -790,8 +764,8 @@ task ScatterIntervalList {
}
runtime {
- docker: dockerImage
memory: memory
+ docker: dockerImage
}
}
@@ -804,7 +778,7 @@ task SortSam {
Int maxRecordsInRam = 500000
Int compressionLevel = 1
- # Default ram of 4 GB. Using 125001.0 to prevent an answer of
+ # Default ram of 4 GB. Using 125001.0 to prevent an answer of
# 4.000000001 which gets rounded to 5.
# GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778
Int XmxGb = ceil(maxRecordsInRam / 125001.0)
@@ -840,13 +814,16 @@ task SortSam {
}
parameter_meta {
- inputBam: {description: "The unsorted input BAM file", category: "required"}
+ # inputs
+ inputBam: {description: "The unsorted input BAM file.", category: "required"}
outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
- XmxGb: {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"}
+ sortByName: {description: "Sort the output file by name, default is position.", category: "advanced"}
+ createMd5File: {description: "Whether to create an MD5 digest for any BAM or FASTQ files created.", category: "advanced"}
+ maxRecordsInRam: {description: "This will specify the number of records stored in RAM before spilling to disk.", category: "advanced"}
+ compressionLevel: {description: "Compression level for all compressed files created.", category: "advanced"}
+ XmxGb: {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"}
+ 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"}
}
}
@@ -854,10 +831,11 @@ task SortVcf {
input {
Array[File]+ vcfFiles
String outputVcfPath
+
File? dict
- String memory = "9G"
String javaXmx = "8G"
+ String memory = "9G"
Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
@@ -879,9 +857,9 @@ task SortVcf {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -889,13 +867,10 @@ task SortVcf {
vcfFiles: {description: "The VCF files to merge and sort.", category: "required"}
outputVcfPath: {description: "The location the sorted VCF files should be written to.", category: "required"}
dict: {description: "A sequence dictionary matching the VCF files.", category: "advanced"}
-
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
+ 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"}
}
}
@@ -904,8 +879,9 @@ task RenameSample {
File inputVcf
String outputPath = "./picard/renamed.vcf"
String newSampleName
- String memory = "9G"
+
String javaXmx = "8G"
+ String memory = "9G"
Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
}
@@ -925,9 +901,9 @@ task RenameSample {
}
runtime {
- docker: dockerImage
- time_minutes: timeMinutes
memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -935,8 +911,8 @@ task RenameSample {
inputVcf: {description: "The VCF file to process.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
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"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", 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"}
}
diff --git a/rtg.wdl b/rtg.wdl
index 104a5ef..bfd3295 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -22,13 +22,14 @@ version 1.0
task Format {
input {
+ Array[File]+ inputFiles
String format = "fasta"
String outputPath = "seq_data.sdf"
- Array[File]+ inputFiles
- String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
+
String rtgMem = "8G"
String memory = "9G"
Int timeMinutes = 1 + ceil(size(inputFiles) * 2)
+ String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
}
command {
@@ -44,21 +45,20 @@ task Format {
}
runtime {
- docker: dockerImage
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- 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"}
+ # inputs
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"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ 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"}
+ 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"}
- rtgMem: {description: "The amount of memory rtg will allocate to the JVM", 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"}
}
}
@@ -68,18 +68,20 @@ task VcfEval {
File baselineIndex
File calls
File callsIndex
- File? evaluationRegions
- File? bedRegions
+ Boolean squashPloidy = false
+ String outputMode = "split"
String outputDir = "output/"
File template
Boolean allRecords = false
Boolean decompose = false
Boolean refOverlap = false
+
+ File? evaluationRegions
+ File? bedRegions
String? sample
- Boolean squashPloidy = false
- String outputMode = "split"
- Int threads = 1 # tool default is number of cores in the system 😱
+
String rtgMem = "8G"
+ Int threads = 1 # Tool default is number of cores in the system 😱.
String memory = "9G"
Int timeMinutes = 1 + ceil(size([baseline, calls], "G") * 5)
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
@@ -132,39 +134,32 @@ task VcfEval {
}
runtime {
- docker: dockerImage
cpu: threads
memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
- baseline: {description: "VCF file containing baseline variants", category: "required"}
- baselineIndex: {description: "The baseline's VCF index", category: "required"}
- calls: {description: "VCF file containing called variants", category: "required"}
- callsIndex: {description: "The call's VCF index", category: "required"}
- outputDir: {description: "Directory for output", category: "advanced"}
- bedRegions: {description: "if set, only read VCF records that overlap the ranges contained in the specified BED file", category: "advanced"}
- evaluationRegions: {description: "if set, evaluate within regions contained in the supplied BED file, allowing transborder matches. To be used for truth-set high-confidence regions or other regions of interest where region boundary effects should be minimized",
- category: "advanced"}
- template: {description: "SDF of the reference genome the variants are called against", category: "required"}
- allRecords: {description: "use all records regardless of FILTER status (Default is to only process records where FILTER is \".\" or \"PASS\")",
- category: "common"}
- decompose: {description: "decompose complex variants into smaller constituents to allow partial credit", category: "common"}
- refOverlap: {description: "allow alleles to overlap where bases of either allele are same-as-ref (Default is to only allow VCF anchor base overlap)",
- category: "common"}
- sample: {description: "the name of the sample to select. Use <baseline_sample>,<calls_sample> to select different sample names for baseline and calls. (Required when using multi-sample VCF files)",
- category: "common"}
- squashPloidy: {description: "treat heterozygous genotypes as homozygous ALT in both baseline and calls, to allow matches that ignore zygosity differences",
- category: "common"}
- outputMode: {description: "output reporting mode. Allowed values are [split, annotate, combine, ga4gh, roc-only] (Default is split)",
- category: "advanced"}
- 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"}
+ # inputs
+ baseline: {description: "VCF file containing baseline variants.", category: "required"}
+ baselineIndex: {description: "The baseline's VCF index.", category: "required"}
+ calls: {description: "VCF file containing called variants.", category: "required"}
+ callsIndex: {description: "The call's VCF index.", category: "required"}
+ squashPloidy: {description: "treat heterozygous genotypes as homozygous ALT in both baseline and calls, to allow matches that ignore zygosity differences.", category: "common"}
+ outputMode: {description: "output reporting mode. Allowed values are [split, annotate, combine, ga4gh, roc-only] (Default is split).", category: "advanced"}
+ outputDir: {description: "Directory for output.", category: "advanced"}
+ template: {description: "SDF of the reference genome the variants are called against.", category: "required"}
+ allRecords: {description: "use all records regardless of FILTER status (Default is to only process records where FILTER is \".\" or \"PASS\").", category: "common"}
+ decompose: {description: "decompose complex variants into smaller constituents to allow partial credit.", category: "common"}
+ refOverlap: {description: "allow alleles to overlap where bases of either allele are same-as-ref (Default is to only allow VCF anchor base overlap).", category: "common"}
+ sample: {description: "the name of the sample to select. Use <baseline_sample>,<calls_sample> to select different sample names for baseline and calls. (Required when using multi-sample VCF files).", category: "common"}
+ bedRegions: {description: "if set, only read VCF records that overlap the ranges contained in the specified BED file.", category: "advanced"}
+ evaluationRegions: {description: "if set, evaluate within regions contained in the supplied BED file, allowing transborder matches. To be used for truth-set high-confidence regions or other regions of interest where region boundary effects should be minimized.", category: "advanced"}
+ rtgMem: {description: "The amount of memory rtg will allocate to the JVM.", category: "advanced"}
+ threads: {description: "Number of threads. Default is 1.", 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/sambamba.wdl b/sambamba.wdl
index cd8da21..df5ab4d 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -20,29 +20,31 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
-
task Markdup {
input {
Array[File] inputBams
String outputPath
- # Sambamba scales like this: 1 thread is fully utilized (1). 2 threads 1.8 utilized. 3 -> 2.4, 4-> 2.7.
- # 2 threads reduces wall clock time by more than 40%.
- Int threads = 2
Int compressionLevel = 1
- Int? hashTableSize
- Int? overFlowListSize
- # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1
+ # sortBufferSize and ioBufferSize taken from markdup defaults as of sambamba 0.7.1.
Int sortBufferSize = 2048
Int ioBufferSize = 128
- Boolean removeDuplicates = false
+ Boolean removeDuplicates = false
+ Int? hashTableSize
+ Int? overFlowListSize
+
+ # Sambamba scales like this: 1 thread is fully utilized (1).
+ # 2 threads 1.8 utilized. 3 -> 2.4, 4-> 2.7.
+ # 2 threads reduces wall clock time by more than 40%.
+ Int threads = 2
# According to the manual sambamba markdup uses the sortbufferSize + 2 times the ioBuffer size.
# Added 1024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
- String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
# Time minute calculation does not work well for higher number of threads.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8) / threads
+ String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
}
+
String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
command {
@@ -57,7 +59,7 @@ task Markdup {
~{"--sort-buffer-size " + sortBufferSize} \
~{"--io-buffer-size " + ioBufferSize} \
~{sep=' ' inputBams} ~{outputPath}
- # sambamba creates an index for us
+ # sambamba creates an index for us.
mv ~{outputPath}.bai ~{bamIndexPath}
}
@@ -67,8 +69,8 @@ task Markdup {
}
runtime {
- memory: "~{memoryMb}M"
cpu: threads
+ memory: "~{memoryMb}M"
time_minutes: timeMinutes
docker: dockerImage
}
@@ -78,17 +80,19 @@ task Markdup {
inputBams: {description: "The input BAM files.", category: "required"}
outputPath: {description: "Output directory path + output file.", category: "required"}
compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- memoryMb: {description: "The amount of memory available to the job in megabytes.", category: "advanced"}
- removeDuplicates: {description: "Whether to remove the duplicates (instead of only marking them).", category: "advanced"}
- hashTableSize: {description: "Sets sambamba's hash table size", category: "advanced"}
- overFlowListSize: {description: "Sets sambamba's overflow list size", category: "advanced"}
- sortBufferSize: {description: "The amount of mb allocated to the sort buffer", category: "advanced"}
+ sortBufferSize: {description: "The amount of mb allocated to the sort buffer.", category: "advanced"}
ioBufferSize: {description: "The amount of mb allocated to each IO buffer. Sambamba uses two IO buffers.", 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"}
+ removeDuplicates: {description: "Whether to remove the duplicates (instead of only marking them).", category: "advanced"}
+ hashTableSize: {description: "Sets sambamba's hash table size.", category: "advanced"}
+ overFlowListSize: {description: "Sets sambamba's overflow list size.", category: "advanced"}
threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ memoryMb: {description: "The amount of memory available to the job in megabytes.", 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
outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
}
}
@@ -98,14 +102,15 @@ task Sort {
String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
Boolean sortByName = false
Int compressionLevel = 1
- Int threads = 1
+
Int memoryPerThreadGb = 4
+ Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb
- String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3)
+ String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
}
- # Select first needed as outputPath is optional input. (bug in cromwell)
+ # Select first needed as outputPath is optional input (bug in cromwell).
String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
command {
@@ -118,7 +123,7 @@ task Sort {
-m ~{memoryPerThreadGb}G \
-o ~{outputPath} \
~{inputBam}
- # sambamba creates an index for us
+ # sambamba creates an index for us.
mv ~{outputPath}.bai ~{bamIndexPath}
}
@@ -140,12 +145,14 @@ task Sort {
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"}
- memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
- memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", 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"}
+ memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes.", category: "advanced"}
threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
+ memoryGb: {description: "The amount of memory available to the job 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"}
+
# outputs
outputBam: {description: "Sorted BAM file."}
+ outputBamIndex: {description: "Sorted BAM file index."}
}
-}
\ No newline at end of file
+}
--
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