diff --git a/hisat2.wdl b/hisat2.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..1e76b17955652ac5cc585619c39351411ef28c7e
--- /dev/null
+++ b/hisat2.wdl
@@ -0,0 +1,47 @@
+version 1.0
+
+task Hisat2 {
+ input {
+ File indexDirectory
+ String indexBasename
+ File inputR1
+ File? inputR2
+ String outputBam
+ String sample
+ String library
+ String readgroup
+ String platform = "illumina"
+ Boolean downstreamTranscriptomeAssembly = true
+
+ Int threads = 1
+ Int memory = 48
+ String dockerTag = "2388ff67fc407dad75774291ca5038f40cac4be0-0"
+ }
+
+ command {
+ set -e -o pipefail
+ mkdir -p $(dirname ~{outputBam})
+ hisat2 \
+ -p ~{threads} \
+ -x ~{indexDirectory}/~{indexBasename} \
+ ~{true="-1" false="-U" defined(inputR2)} ~{inputR1} \
+ ~{"-2" + inputR2} \
+ --rg-id ~{readgroup} \
+ --rg 'SM:~{sample}' \
+ --rg 'LB:~{library}' \
+ --rg 'PL:~{platform}' \
+ ~{true="--dta" false="" downstreamTranscriptomeAssembly} \
+ | samtools sort > ~{outputBam}
+
+ }
+
+ output {
+ File bamFile = outputBam
+ }
+
+ runtime {
+ memory: (memory / threads) + 1
+ cpu: threads + 1
+ docker: "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:" + dockerTag
+ }
+}
\ No newline at end of file
diff --git a/picard.wdl b/picard.wdl
index 948240dc299a424811c062135f58b32a0627f2be..514ec1d9b9bbf776913cc8d88e78c8a99dca2d95 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -4,26 +4,20 @@ import "common.wdl"
task BedToIntervalList {
input {
- String? preCommand
- File? picardJar
-
File bedFile
File dict
String outputPath
Int memory = 4
Float memoryMultiplier = 3.0
- }
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
+ String dockerTag = "2.18.26--0"
+ }
command {
set -e -o pipefail
mkdir -p $(dirname "~{outputPath}")
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
BedToIntervalList \
I=~{bedFile} \
O=~{outputPath} \
@@ -35,13 +29,13 @@ task BedToIntervalList {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task CollectMultipleMetrics {
input {
- String? preCommand
IndexedBamFile bamFile
Reference reference
String basename
@@ -56,21 +50,16 @@ task CollectMultipleMetrics {
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
- String? picardJar
-
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
mkdir -p $(dirname "~{basename}")
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
CollectMultipleMetrics \
I=~{bamFile.file} \
R=~{reference.fasta} \
@@ -109,33 +98,30 @@ task CollectMultipleMetrics {
}
runtime {
+ # https://raw.githubusercontent.com/BioContainers/multi-package-containers/80886dfea00f3cd9e7ae2edf4fc42816a10e5403/combinations/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923%3A8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0.tsv
+ # Contains r-base=3.4.1,picard=2.18.2
+ docker: "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task CollectRnaSeqMetrics {
input {
- String? preCommand
IndexedBamFile bamFile
File refRefflat
String basename
String strandSpecificity = "NONE"
- String? picardJar
-
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
mkdir -p $(dirname "~{basename}")
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
CollectRnaSeqMetrics \
I=~{bamFile.file} \
O=~{basename}.RNA_Metrics \
@@ -150,34 +136,31 @@ task CollectRnaSeqMetrics {
}
runtime {
+ # https://raw.githubusercontent.com/BioContainers/multi-package-containers/80886dfea00f3cd9e7ae2edf4fc42816a10e5403/combinations/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923%3A8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0.tsv
+ # Contains r-base=3.4.1,picard=2.18.2
+ docker: "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task CollectTargetedPcrMetrics {
input {
- String? preCommand
IndexedBamFile bamFile
Reference reference
File ampliconIntervals
Array[File]+ targetIntervals
String basename
- String? picardJar
-
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
mkdir -p $(dirname "~{basename}")
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
CollectTargetedPcrMetrics \
I=~{bamFile.file} \
R=~{reference.fasta} \
@@ -195,6 +178,7 @@ task CollectTargetedPcrMetrics {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
@@ -202,24 +186,18 @@ task CollectTargetedPcrMetrics {
# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
task GatherBamFiles {
input {
- String? preCommand
Array[File]+ inputBams
Array[File]+ inputBamsIndex
String outputBamPath
- String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
GatherBamFiles \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
@@ -236,30 +214,25 @@ task GatherBamFiles {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task GatherVcfs {
input {
- String? preCommand
Array[File]+ inputVcfs
Array[File]+ inputVcfIndexes
String outputVcfPath
- String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
GatherVcfs \
INPUT=~{sep=' INPUT=' inputVcfs} \
OUTPUT=~{outputVcfPath}
@@ -270,6 +243,7 @@ task GatherVcfs {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
@@ -277,15 +251,14 @@ task GatherVcfs {
# Mark duplicate reads to avoid counting non-independent observations
task MarkDuplicates {
input {
- String? preCommand
Array[File]+ inputBams
Array[File] inputBamIndexes
String outputBamPath
String metricsPath
- String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--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
@@ -297,15 +270,10 @@ task MarkDuplicates {
# 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"
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
mkdir -p $(dirname ~{outputBamPath})
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
MarkDuplicates \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
@@ -329,6 +297,7 @@ task MarkDuplicates {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
@@ -336,28 +305,22 @@ task MarkDuplicates {
# Combine multiple VCFs or GVCFs from scattered HaplotypeCaller runs
task MergeVCFs {
input {
- String? preCommand
Array[File]+ inputVCFs
Array[File]+ inputVCFsIndexes
String outputVcfPath
Int? compressionLevel
- String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
# Using MergeVcfs instead of GatherVcfs so we can create indices
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
MergeVcfs \
INPUT=~{sep=' INPUT=' inputVCFs} \
OUTPUT=~{outputVcfPath}
@@ -371,31 +334,26 @@ task MergeVCFs {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task SamToFastq {
input {
- String? preCommand
IndexedBamFile inputBam
String outputRead1
String? outputRead2
String? outputUnpaired
- String? picardJar
Int memory = 16 # High memory default to avoid crashes.
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
SamToFastq \
I=~{inputBam.file} \
~{"FASTQ=" + outputRead1} \
@@ -410,30 +368,25 @@ task SamToFastq {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task ScatterIntervalList {
input {
- String? preCommand
File interval_list
Int scatter_count
- String? picardJar
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
mkdir scatter_list
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
IntervalListTools \
SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
@@ -449,31 +402,26 @@ task ScatterIntervalList {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
task SortVcf {
input {
- String? preCommand
- String? picardJar
-
Array[File]+ vcfFiles
String outputVcfPath
File? dict
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "2.18.26--0"
}
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
+ picard -Xmx~{memory}G \
SortVcf \
I=~{sep=" I=" vcfFiles} \
~{"SEQUENCE_DICTIONARY=" + dict} \
@@ -488,6 +436,7 @@ task SortVcf {
}
runtime {
+ docker: "quay.io/biocontainers/picard:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
\ No newline at end of file