Skip to content
Snippets Groups Projects
Unverified Commit f27a750c authored by Ruben Vorderman's avatar Ruben Vorderman Committed by GitHub
Browse files

Merge branch 'develop' into BIOWDL-194

parents edfcd38d 37442743
No related branches found
No related tags found
1 merge request!89allow for additional annotations to be added into mergecounts output
Hide whitespace changes
Inline Side-by-side
hisat2.wdl 0 → 100644
+ 47
− 0
View file @ f27a750c
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
picard.wdl
+ 38
− 89
View file @ f27a750c
......@@ -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
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment