diff --git a/CPAT.wdl b/CPAT.wdl
index 0c4e83db1f67d2a5fca475af8adb3076e73ed3d9..b92053d1e1fcdbe116fc845c845442fd1b7aeecc 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -11,7 +11,7 @@ task CPAT {
# CPAT should not index the reference genome.
Array[String]? startCodons
Array[String]? stopCodons
- String dockerTag = "v1.2.4_cv1"
+ String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
}
# Some WDL magic in the command section to properly output the start and stopcodons to the command.
@@ -34,7 +34,7 @@ task CPAT {
}
runtime {
- docker: "biocontainers/cpat:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 15f0771381d81ae668aaf25d8e173b3551bfd8d9..d88f0610723528fbc0ad1d1c9648147eca226a3f 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -230,7 +230,8 @@ task ReorderGlobbedScatters {
task ScatterRegions {
input {
- Reference reference
+ File referenceFasta
+ File referenceFastaDict
Int? scatterSize
File? regions
Boolean notSplitContigs = false
@@ -239,7 +240,7 @@ task ScatterRegions {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerTag = "0.2--0"
+ String dockerImage = "quay.io/biocontainers/biopet-scatterregions:0.2--0"
}
# OutDirPath must be defined here because the glob process relies on
@@ -251,7 +252,7 @@ task ScatterRegions {
set -e -o pipefail
mkdir -p ~{outputDirPath}
biopet-scatterregions -Xmx~{memory}G \
- -R ~{reference.fasta} \
+ -R ~{referenceFasta} \
-o ~{outputDirPath} \
~{"-s " + scatterSize} \
~{"-L " + regions} \
@@ -264,7 +265,7 @@ task ScatterRegions {
}
runtime {
- docker: "quay.io/biocontainers/biopet-scatterregions:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
diff --git a/bwa.wdl b/bwa.wdl
index e45c4dbc31de14114c9e3feb84938fa62e3ff3d7..2fe22007cd2e1d739950ed32a42aba6f429e7722 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -13,7 +13,9 @@ task Mem {
Int threads = 2
Int memory = 8
Int picardMemory = 4
- String dockerTag = "43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0"
+ # 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"
}
command {
@@ -40,10 +42,7 @@ task Mem {
runtime{
cpu: threads
memory: memory + picardMemory + picardMemory
- # 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)
- docker: "quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:" +
- dockerTag
+ docker: dockerImage
}
}
diff --git a/collect-columns.wdl b/collect-columns.wdl
index 68c9dcc884563d41e6322440e2f0743368c65ef7..910aeac255dc07afc22068896d69aa81ef56fed8 100644
--- a/collect-columns.wdl
+++ b/collect-columns.wdl
@@ -13,10 +13,12 @@ task CollectColumns {
File? referenceGtf
String? featureAttribute
- String dockerTag = "0.2.0--py_1"
+ String dockerImage = "quay.io/biocontainers/collect-columns:0.2.0--py_1"
}
command {
+ set -e
+ mkdir -p $(dirname ~{outputPath})
collect-columns \
~{outputPath} \
~{sep=" " inputTables} \
@@ -36,6 +38,6 @@ task CollectColumns {
runtime {
memory: 4 + ceil(0.5* length(inputTables))
- docker: "quay.io/biocontainers/collect-columns:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 703e990c1e452db8b3aacb80b847f2727bea101b..6161d8baf3721b1e93fc006e9f6761ee5e695285 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -62,8 +62,8 @@ task Cutadapt {
String? reportPath
Int cores = 1
- Int memory = 16
- String dockerTag = "2.3--py36h14c3975_0"
+ Int memory = 16 # FIXME: Insane memory. Double-check if needed.
+ String dockerImage = "quay.io/biocontainers/cutadapt:2.3--py36h14c3975_0"
}
String read2outputArg = if (defined(read2output))
@@ -168,6 +168,6 @@ task Cutadapt {
runtime {
cpu: cores
memory: memory
- docker: "quay.io/biocontainers/cutadapt:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index ad9e224694fffaa5d6860fa55c912a188ed9e0da..d4386b8198c2d7965cd8653d732d67469ab419b9 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -18,7 +18,7 @@ task Fastqc {
String? dir
Int threads = 1
- String dockerTag = "0.11.7--4"
+ String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4"
Array[File]? NoneArray
File? NoneFile
}
@@ -61,7 +61,7 @@ task Fastqc {
runtime {
cpu: threads
- docker: "quay.io/biocontainers/fastqc:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/fastqsplitter.wdl b/fastqsplitter.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..66f79af605d4f3bd9f28c3fa7690bb9808a5147c
--- /dev/null
+++ b/fastqsplitter.wdl
@@ -0,0 +1,62 @@
+version 1.0
+
+# MIT License
+#
+# Copyright (c) 2019 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# 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 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
+# 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 Fastqsplitter {
+ input {
+ File inputFastq
+ Array[String]+ outputPaths
+ String dockerImage = "quay.io/biocontainers/fastqsplitter:1.0.0--py_0"
+ Int? compressionLevel
+ Int? threadsPerFile
+ # fastqplitter utilizes one thread per input file and one or more threads per output file + one thread for the application.
+ # Since a compression level of 1 is used, each output file uses approx 0.5 cores.
+ Int cores = 1 + ceil(0.5 * length(outputPaths))
+ }
+
+ command {
+ set -e
+ mkdir -p $(dirname ~{sep=' ' outputPaths})
+ fastqsplitter \
+ ~{"-c " + compressionLevel} \
+ ~{"-t " + threadsPerFile} \
+ -i ~{inputFastq} \
+ -o ~{sep=' -o ' outputPaths}
+ }
+
+ output {
+ Array[File] chunks = outputPaths
+ }
+
+ # Using very safe margins here. 10MB/300MB per outputfile is used for single-threaded/multi-threaded compression.
+ Float memoryPerFile = if select_first([threadsPerFile, 1]) > 1 then 0.40 else 0.02
+ Int fastqsplitterMemory = ceil(0.100 + memoryPerFile * length(outputPaths))
+ # Make sure a minimum of 2 GB is present to pull the singularity image
+ Int memory = if fastqsplitterMemory <= 2 then 2 else fastqsplitterMemory
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ cpu: cores
+ }
+}
diff --git a/gatk.wdl b/gatk.wdl
index e76a93e8c979c6ebee0e8857d669da2e13827458..87fa1046be22020b0a7b37b638d6c30084c43519 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -14,7 +14,7 @@ task ApplyBQSR {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -42,7 +42,7 @@ task ApplyBQSR {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -64,7 +64,7 @@ task BaseRecalibrator {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
Array[File]+ knownIndelsSitesVCFsArg = flatten([
@@ -90,7 +90,7 @@ task BaseRecalibrator {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -107,7 +107,7 @@ task CombineGVCFs {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -127,7 +127,7 @@ task CombineGVCFs {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -140,7 +140,7 @@ task GatherBqsrReports {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -157,7 +157,7 @@ task GatherBqsrReports {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -175,7 +175,7 @@ task GenotypeGVCFs {
File? dbsnpVCFIndex
Int memory = 6
Float memoryMultiplier = 2.0
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -200,7 +200,7 @@ task GenotypeGVCFs {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -220,7 +220,7 @@ task HaplotypeCallerGvcf {
File? dbsnpVCFIndex
Int memory = 4
Float memoryMultiplier = 3
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -243,7 +243,7 @@ task HaplotypeCallerGvcf {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -258,11 +258,12 @@ task MuTect2 {
String outputVcf
String tumorSample
String? normalSample
+ File? panelOfNormals
Array[File]+ intervals
Int memory = 4
Float memoryMultiplier = 3
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -274,6 +275,7 @@ task MuTect2 {
-I ~{sep=" -I " inputBams} \
-tumor ~{tumorSample} \
~{"-normal " + normalSample} \
+ ~{"--panel-of-normals " + panelOfNormals} \
-O ~{outputVcf} \
-L ~{sep=" -L " intervals}
}
@@ -284,7 +286,7 @@ task MuTect2 {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -301,7 +303,7 @@ task SplitNCigarReads {
Int memory = 4
Float memoryMultiplier = 4
- String dockerTag = "4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
@@ -321,7 +323,7 @@ task SplitNCigarReads {
}
runtime {
- docker: "quay.io/biocontainers/gatk4:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index 51fec85b600ae7c0df5c96683a9458901e0759cf..eea15236e77ea0551665f1014055010461d621bf 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -2,7 +2,7 @@ version 1.0
task GffCompare {
input {
- String dockerTag = "0.10.6--h2d50403_0"
+ String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
File? inputGtfList
Array[File] inputGtfFiles
File referenceAnnotation
@@ -87,6 +87,6 @@ task GffCompare {
}
runtime {
- docker: "quay.io/biocontainers/gffcompare:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
diff --git a/gffread.wdl b/gffread.wdl
index 08b2e8d7cc8195edd0da76a83625a5c91292f58d..da99781b99529b4e452ae301a6eb2e67c6e2ccaf 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -10,7 +10,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
Boolean outputGtfFormat = false
- String dockerTag = "0.9.12--0"
+ String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
# The mkdirs below are hackish. It should be
@@ -41,6 +41,6 @@ task GffRead {
}
runtime {
- docker: "quay.io/biocontainers/gffread:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
diff --git a/hisat2.wdl b/hisat2.wdl
index 0c8417f7ae3592e863477d251a550b7f8457feca..27d9dedf62519f395576168286d7aab7a3b0c5f8 100644
--- a/hisat2.wdl
+++ b/hisat2.wdl
@@ -14,8 +14,10 @@ task Hisat2 {
Int threads = 1
Int memory = 48
+ # quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
+ # is a combination of hisat2 and samtools
# hisat2=2.1.0, samtools=1.8
- String dockerTag = "2388ff67fc407dad75774291ca5038f40cac4be0-0"
+ String dockerImage = "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2388ff67fc407dad75774291ca5038f40cac4be0-0"
}
command {
@@ -41,8 +43,6 @@ task Hisat2 {
runtime {
memory: (memory / threads) + 1
cpu: threads + 1
- # quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
- # is a combination of hisat2 and samtools
- docker: "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
diff --git a/htseq.wdl b/htseq.wdl
index a687a8a6242b4ec0a8b1dd2b3b46b5a2c49d3923..ed13167cc800627a8370634d667f96022c3bfe5a 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -11,7 +11,7 @@ task HTSeqCount {
String stranded = "no"
Int memory = 40
- String dockerTag = "0.9.1--py36h7eb728f_2"
+ String dockerImage = "quay.io/biocontainers/htseq:0.9.1--py36h7eb728f_2"
}
command {
@@ -32,6 +32,6 @@ task HTSeqCount {
runtime {
memory: memory
- docker: "quay.io/biocontainers/htseq:" + dockerTag
+ docker: dockerImage
}
}
\ No newline at end of file
diff --git a/manta.wdl b/manta.wdl
index 759766e33797cbb3479dcf256331709c18fd27f4..f2e1d43d37947ed71c48de543683079fce9bf8a5 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -4,31 +4,28 @@ import "common.wdl"
task Somatic {
input {
- IndexedBamFile tumorBam
- IndexedBamFile? normalBam
- Reference reference
- String runDir
+ File tumorBam
+ File tumorBamIndex
+ File? normalBam
+ File? normalBamIndex
+ File referenceFasta
+ File referenceFastaFai
+ String runDir = "./manta_run"
File? callRegions
File? callRegionsIndex
Boolean exome = false
Int cores = 1
Int memory = 4
- String dockerTag = "1.4.0--py27_1"
+ String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
- File? doNotDefineThis #FIXME
}
- File? normalBamFile = if defined(normalBam)
- then select_first([normalBam]).file
- else doNotDefineThis
-
command {
- set -e
configManta.py \
- ~{"--normalBam " + normalBamFile} \
- ~{"--tumorBam " + tumorBam.file} \
- --referenceFasta ~{reference.fasta} \
+ ~{"--normalBam " + normalBam} \
+ ~{"--tumorBam " + tumorBam} \
+ --referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
@@ -40,25 +37,16 @@ task Somatic {
}
output {
- IndexedVcfFile candidateSmallIndels = object {
- file: runDir + "/results/variants/candidateSmallIndels.vcf.gz",
- index: runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
- }
- IndexedVcfFile candidateSV = object {
- file: runDir + "/results/variants/candidateSV.vcf.gz",
- index: runDir + "/results/variants/candidateSV.vcf.gz.tbi"
- }
- IndexedVcfFile tumorSV = if defined(normalBam)
- then object {
- file: runDir + "/results/variants/somaticSV.vcf.gz",
- index: runDir + "/results/variants/somaticSV.vcf.gz.tbi"
- }
- else object {
- file: runDir + "/results/variants/tumorSV.vcf.gz",
- index: runDir + "/results/variants/tumorSV.vcf.gz.tbi"
- }
-
- #FIXME: workaround for https://github.com/broadinstitute/cromwell/issues/4111
+ File candidateSmallIndelsVcf = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
+ File candidateSmallIndelsVcfIndex = runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+ File candidateSVVcf = runDir + "/results/variants/candidateSV.vcf.gz"
+ File candidatSVVcfIndex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+ File tumorSVVcf = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz"
+ else runDir + "/results/variants/tumorSV.vcf.gz"
+ File tumorSVVcfIndex = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
+ else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
@@ -66,6 +54,6 @@ task Somatic {
runtime {
cpu: cores
memory: memory
- docker: "quay.io/biocontainers/manta:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/multiqc.wdl b/multiqc.wdl
index 76563a494f1998eab5b2f83ac42e5bf7e81a47fe..e7a87e1490931ea84ccf156aa4c54f349d668292 100644
--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -2,7 +2,7 @@ version 1.0
task MultiQC {
input {
- String dockerTag = "1.7--py_1"
+ String dockerImage = "quay.io/biocontainers/multiqc:1.7--py_1"
# Use a string here so cromwell does not relocate an entire analysis directory
String analysisDirectory
Array[File] dependencies = [] # This must be used in order to run multiqc after these tasks.
@@ -86,6 +86,6 @@ task MultiQC {
}
runtime {
- docker: "quay.io/biocontainers/multiqc:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/picard.wdl b/picard.wdl
index a0a29fa1da46a5ce865f677049d7779da2988656..182797218ade65f4213b2f252bb5ae371bab69ef 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -8,7 +8,7 @@ task BedToIntervalList {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
command {
@@ -26,7 +26,7 @@ task BedToIntervalList {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -52,7 +52,9 @@ task CollectMultipleMetrics {
Int memory = 8
Float memoryMultiplier = 4
- String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
+ # 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
+ String dockerImage = "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
@@ -109,6 +111,7 @@ task CollectMultipleMetrics {
insertSizeHistogramPdf,
insertSize,
preAdapterDetail,
+ preAdapterSummary,
qualityByCycle,
qualityByCyclePdf,
qualityDistribution,
@@ -118,9 +121,8 @@ 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
+
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -135,7 +137,9 @@ task CollectRnaSeqMetrics {
Int memory = 8
Float memoryMultiplier = 4.0
- String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
+ # 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
+ String dockerImage = "quay.io/biocontainers/mulled-v2-23d9f7c700e78129a769e78521eb86d6b8341923:8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
command {
@@ -156,9 +160,7 @@ 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
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -176,7 +178,7 @@ task CollectTargetedPcrMetrics {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
command {
@@ -200,7 +202,7 @@ task CollectTargetedPcrMetrics {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -214,7 +216,7 @@ task GatherBamFiles {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
command {
@@ -235,7 +237,7 @@ task GatherBamFiles {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -248,7 +250,7 @@ task GatherVcfs {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
command {
@@ -265,7 +267,7 @@ task GatherVcfs {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -280,7 +282,7 @@ task MarkDuplicates {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard: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
@@ -319,7 +321,7 @@ task MarkDuplicates {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -333,7 +335,7 @@ task MergeVCFs {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
# Using MergeVcfs instead of GatherVcfs so we can create indices
@@ -354,7 +356,7 @@ task MergeVCFs {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -403,7 +405,7 @@ task ScatterIntervalList {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
command {
@@ -425,7 +427,7 @@ task ScatterIntervalList {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
@@ -438,7 +440,7 @@ task SortVcf {
Int memory = 8
Float memoryMultiplier = 3.0
- String dockerTag = "2.18.26--0"
+ String dockerImage = "quay.io/biocontainers/picard:2.18.26--0"
}
@@ -458,7 +460,7 @@ task SortVcf {
}
runtime {
- docker: "quay.io/biocontainers/picard:" + dockerTag
+ docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
}
\ No newline at end of file
diff --git a/samtools.wdl b/samtools.wdl
index 3b0024683cff468e19076ba597f2661694dea9ef..09f3fc4100b516748196f728061883cdd17b13d8 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -6,13 +6,14 @@ task BgzipAndIndex {
String outputDir
String type = "vcf"
- String dockerTag = "0.2.6--ha92aebf_0"
+ String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
}
String outputGz = outputDir + "/" + basename(inputFile) + ".gz"
command {
set -e
+ mkdir -p $(dirname ~{outputGz})
bgzip -c ~{inputFile} > ~{outputGz}
tabix ~{outputGz} -p ~{type}
}
@@ -23,29 +24,40 @@ task BgzipAndIndex {
}
runtime {
- docker: "quay.io/biocontainers/tabix:" + dockerTag
+ docker: dockerImage
}
}
task Index {
input {
File bamFile
- String bamIndexPath
-
- String dockerTag = "1.8--h46bd0b3_5"
+ String outputBamPath = basename(bamFile)
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
+ # Select_first is needed, otherwise womtool validate fails.
+ String bamIndexPath = sub(select_first([outputBamPath]), "\.bam$", ".bai")
+
command {
- samtools index ~{bamFile} ~{bamIndexPath}
+ bash -c '
+ set -e
+ # Make sure outputBamPath does not exist.
+ if [ ! -f ~{outputBamPath} ]
+ then
+ mkdir -p $(dirname ~{outputBamPath})
+ ln ~{bamFile} ~{outputBamPath}
+ fi
+ samtools index ~{outputBamPath} ~{bamIndexPath}
+ '
}
output {
- File indexedBam = bamFile
- File index = bamIndexPath
+ File indexedBam = outputBamPath
+ File index = bamIndexPath
}
runtime {
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
}
@@ -55,7 +67,7 @@ task Merge {
String outputBamPath = "merged.bam"
Boolean force = true
- String dockerTag = "1.8--h46bd0b3_5"
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
String indexPath = sub(outputBamPath, "\.bam$",".bai")
@@ -72,7 +84,7 @@ task Merge {
}
runtime {
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
}
@@ -81,10 +93,12 @@ task Markdup {
File inputBam
String outputBamPath
- String dockerTag = "1.8--h46bd0b3_5"
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
+ set -e
+ mkdir -p $(dirname ~{outputBamPath})
samtools markdup ~{inputBam} ~{outputBamPath}
}
@@ -93,7 +107,7 @@ task Markdup {
}
runtime {
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
}
@@ -102,7 +116,7 @@ task Flagstat {
File inputBam
String outputPath
- String dockerTag = "1.8--h46bd0b3_5"
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
@@ -116,7 +130,7 @@ task Flagstat {
}
runtime {
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
}
@@ -135,7 +149,7 @@ task Fastq {
Int threads = 1
Int memory = 1
- String dockerTag = "1.8--h46bd0b3_5"
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
@@ -162,7 +176,7 @@ task Fastq {
runtime {
cpu: threads
memory: memory
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
parameter_meta {
@@ -181,7 +195,7 @@ task Tabix {
File inputFile
String outputFilePath = "indexed.vcf.gz"
String type = "vcf"
- String dockerTag = "0.2.6--ha92aebf_0"
+ 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.
command {
@@ -200,7 +214,7 @@ task Tabix {
}
runtime {
- docker: "quay.io/biocontainers/tabix:" + dockerTag
+ docker: dockerImage
}
}
@@ -218,10 +232,12 @@ task View {
Int threads = 1
Int memory = 1
- String dockerTag = "1.8--h46bd0b3_5"
+ String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
command {
+ set -e
+ mkdir -p $(dirname ~{outputFileName})
samtools view \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
@@ -242,6 +258,6 @@ task View {
runtime {
cpu: threads
memory: memory
- docker: "quay.io/biocontainers/samtools:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 77d068191c3299c1a7ef67c79ee220e86c8c8533..d1163b4a1fcda41b45f9e3a12e7eb5b2ad16c882 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -1,7 +1,5 @@
version 1.0
-import "common.wdl" as common
-
task ParallelPaired {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
@@ -9,11 +7,14 @@ task ParallelPaired {
File? classifierSNV
File? classifierIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile tumorBam
- IndexedBamFile normalBam
+ File tumorBam
+ File tumorBamIndex
+ File normalBam
+ File normalBamIndex
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -28,6 +29,7 @@ task ParallelPaired {
File? strelkaIndel
Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
@@ -35,13 +37,13 @@ task ParallelPaired {
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
- --tumor-bam-file ~{tumorBam.file} \
- --normal-bam-file ~{normalBam.file} \
+ --tumor-bam-file ~{tumorBam} \
+ --normal-bam-file ~{normalBam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
@@ -69,7 +71,7 @@ task ParallelPaired {
runtime {
cpu: threads
- docker: "lethalfang/somaticseq:3.1.0"
+ docker: dockerImage
}
}
@@ -80,11 +82,14 @@ task ParallelPairedTrain {
File truthSNV
File truthIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile tumorBam
- IndexedBamFile normalBam
+ File tumorBam
+ File tumorBamIndex
+ File normalBam
+ File normalBamIndex
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -99,6 +104,7 @@ task ParallelPairedTrain {
File? strelkaIndel
Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
@@ -107,13 +113,13 @@ task ParallelPairedTrain {
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
- --tumor-bam-file ~{tumorBam.file} \
- --normal-bam-file ~{normalBam.file} \
+ --tumor-bam-file ~{tumorBam} \
+ --normal-bam-file ~{normalBam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
@@ -139,7 +145,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
- docker: "lethalfang/somaticseq:3.1.0"
+ docker: dockerImage
}
}
@@ -150,10 +156,12 @@ task ParallelSingle {
File? classifierSNV
File? classifierIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile bam
+ File bam
+ File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -162,6 +170,7 @@ task ParallelSingle {
File? strelkaVCF
Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
@@ -169,12 +178,12 @@ task ParallelSingle {
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
- --bam-file ~{bam.file} \
+ --bam-file ~{bam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
@@ -196,7 +205,7 @@ task ParallelSingle {
runtime {
cpu: threads
- docker: "lethalfang/somaticseq:3.1.0"
+ docker: dockerImage
}
}
@@ -207,10 +216,12 @@ task ParallelSingleTrain {
File truthSNV
File truthIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile bam
+ File bam
+ File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -219,6 +230,7 @@ task ParallelSingleTrain {
File? strelkaVCF
Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
@@ -227,12 +239,12 @@ task ParallelSingleTrain {
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
- --bam-file ~{bam.file} \
+ --bam-file ~{bam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
@@ -252,6 +264,6 @@ task ParallelSingleTrain {
runtime {
cpu: threads
- docker: "lethalfang/somaticseq:3.1.0"
+ docker: dockerImage
}
}
diff --git a/star.wdl b/star.wdl
index edc57155ee89b240e7aed5644fc3294159899406..e518715a82dc3b5adab775d3afba4391ec570c70 100644
--- a/star.wdl
+++ b/star.wdl
@@ -16,7 +16,7 @@ task Star {
Int runThreadN = 4
Int memory = 48
- String dockerTag = "2.6.0c--0"
+ String dockerImage = "quay.io/biocontainers/star:2.6.0c--0"
}
#TODO Needs to be extended for all possible output extensions
@@ -48,7 +48,7 @@ task Star {
# Return memory per CPU here due to SGE backend.
# Can also work with slurms mem-per-cpu flag
memory: (memory / runThreadN) + 1
- docker: "quay.io/biocontainers/star:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/strelka.wdl b/strelka.wdl
index 398631100824f8586c970cb327346f8886337e6d..f5cd525df88e1569b17c9f304264fc1cb5d202c1 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -4,10 +4,11 @@ import "common.wdl" as common
task Germline {
input {
- String runDir
+ String runDir = "./strelka_run"
Array[File]+ bams
Array[File]+ indexes
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -15,14 +16,13 @@ task Germline {
Int cores = 1
Int memory = 4
- String dockerTag = "2.9.7--0"
+ String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
}
command {
- set -e
configureStrelkaGermlineWorkflow.py \
--bam ~{sep=" --bam " bams} \
- --ref ~{reference.fasta} \
+ --ref ~{referenceFasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
~{true="--exome" false="" exome} \
@@ -40,7 +40,7 @@ task Germline {
}
runtime {
- docker: "quay.io/biocontainers/strelka:" + dockerTag
+ docker: dockerImage
cpu: cores
memory: memory
}
@@ -48,35 +48,34 @@ task Germline {
task Somatic {
input {
- String runDir
- IndexedBamFile normalBam
- IndexedBamFile tumorBam
- Reference reference
+ String runDir = "./strelka_run"
+ File normalBam
+ File normalBamIndex
+ File tumorBam
+ File tumorBamIndex
+ File referenceFasta
+ File referenceFastaFai
File? callRegions
File? callRegionsIndex
- IndexedVcfFile? indelCandidates
+ File? indelCandidatesVcf
+ File? indelCandidatesVcfIndex
Boolean exome = false
Int cores = 1
Int memory = 4
- String dockerTag = "2.9.7--0"
+ String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
File? doNotDefineThis #FIXME
}
- File? indelCandidatesFile = if (defined(indelCandidates))
- then select_first([indelCandidates]).file
- else doNotDefineThis
-
command {
- set -e
configureStrelkaSomaticWorkflow.py \
- --normalBam ~{normalBam.file} \
- --tumorBam ~{tumorBam.file} \
- --ref ~{reference.fasta} \
+ --normalBam ~{normalBam} \
+ --tumorBam ~{tumorBam} \
+ --ref ~{referenceFasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
- ~{"--indelCandidates " + indelCandidatesFile} \
+ ~{"--indelCandidates " + indelCandidatesVcf} \
~{true="--exome" false="" exome}
~{runDir}/runWorkflow.py \
@@ -93,7 +92,7 @@ task Somatic {
}
runtime {
- docker: "quay.io/biocontainers/strelka:" + dockerTag
+ docker: dockerImage
cpu: cores
memory: memory
}
diff --git a/stringtie.wdl b/stringtie.wdl
index a66101d116f3f5fb64c794307b76bb04f61271dc..9c7c1013c124187ba777629099d92508a68483de 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -1,10 +1,9 @@
version 1.0
-import "common.wdl"
-
task Stringtie {
input {
- IndexedBamFile bamFile
+ File bam
+ File bamIndex
File? referenceGtf
Boolean skipNovelTranscripts = false
String assembledTranscriptsFile
@@ -14,7 +13,7 @@ task Stringtie {
Int threads = 1
Int memory = 10
- String dockerTag = "1.3.4--py35_0"
+ String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
command {
@@ -28,7 +27,7 @@ task Stringtie {
~{true="--fr" false="" secondStranded} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
- ~{bamFile.file}
+ ~{bam}
}
output {
@@ -39,7 +38,7 @@ task Stringtie {
runtime {
cpu: threads
memory: memory
- docker: "quay.io/biocontainers/stringtie:" + dockerTag
+ docker: dockerImage
}
}
@@ -57,7 +56,7 @@ task Merge {
String? label
Int memory = 10
- String dockerTag = "1.3.4--py35_0"
+ String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
command {
@@ -82,6 +81,6 @@ task Merge {
runtime {
memory: memory
- docker: "quay.io/biocontainers/stringtie:" + dockerTag
+ docker: dockerImage
}
}
diff --git a/vardict.wdl b/vardict.wdl
index 05398995ee139420fb40a6dd7983f969c5148a0b..0cbf38acd7a69f22e4b760f7f17932f585a52852 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -5,10 +5,13 @@ import "common.wdl"
task VarDict {
input {
String tumorSampleName
- IndexedBamFile tumorBam
+ File tumorBam
+ File tumorBamIndex
String? normalSampleName
- IndexedBamFile? normalBam
- Reference reference
+ File? normalBam
+ File? normalBamIndex
+ File referenceFasta
+ File referenceFastaFai
File bedFile
String outputVcf
@@ -20,23 +23,18 @@ task VarDict {
Int threads = 1
Int memory = 16
Float memoryMultiplier = 2.5
- String dockerTag = "1.5.8--1"
+ String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
- File? doNotDefineThis #FIXME
}
- File? normalBamFile = if defined(normalBam)
- then select_first([normalBam]).file
- else doNotDefineThis
-
command {
set -e -o pipefail
export JAVA_OPTS="-Xmx~{memory}G"
vardict-java \
~{"-th " + threads} \
- -G ~{reference.fasta} \
+ -G ~{referenceFasta} \
-N ~{tumorSampleName} \
- -b "~{tumorBam.file}~{"|" + normalBamFile}" \
+ -b "~{tumorBam}~{"|" + normalBam}" \
~{true="" false="-z" defined(normalBam)} \
-c ~{chromosomeColumn} \
-S ~{startColumn} \
@@ -57,6 +55,6 @@ task VarDict {
runtime {
cpu: threads + 2
memory: ceil(memory * memoryMultiplier)
- docker: "quay.io/biocontainers/vardict-java:" + dockerTag
+ docker: dockerImage
}
}