diff --git a/CHANGELOG.md b/CHANGELOG.md
index 54c398e0e3348935a99e70380292a0844ada88a9..3fda7d6262af5addd3dd37ac48d909a1187e6e0d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,14 @@ that users understand how the changes affect the new version.
version 2.2.0-dev
---------------------------
++ Add `GenomicsDBImport` task for GATK.
++ Add `annotationGroups` input to `GenotypeGVCFs` to allow setting multiple
+ annotation groups. The `StandardAnnotation` group is still used as default.
++ GenotypeGVCFs, only allow one input GVCF file, as the tool also only allows
+ one input file.
++ Rename HaplotypeCallerGVCF to HaplotypeCaller. Add `gvcf` option to set
+ whether output should be a GVCF.
++ Centrifuge: Add Krona task specific to Centrifuge.
+ Centrifuge: Fix Centrifuge tests, where sometimes the index files could still not be located.
+ Update parameter_meta for TALON, Centrifuge and Minimap2.
+ Centrifuge: Fix issue where Centrifuge Inspect did not get the correct index files location.
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 909de67b9a564fe4a248f070b4873816cb1d465f..a3e7aeaf1f181017f802dc0edd6fc6c37eb60b08 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -37,7 +37,7 @@ task Build {
Int threads = 5
String memory = "20G"
- String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
command {
@@ -107,7 +107,7 @@ task Classify {
Int threads = 4
String memory = "16G"
- String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
Map[String, String] inputFormatOptions = {"fastq": "-q", "fasta": "-f", "qseq": "--qseq", "raw": "-r", "sequences": "-c"}
@@ -184,7 +184,7 @@ task Inspect {
Int? across
String memory = "4G"
- String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he860b03_3"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
Map[String, String] outputOptions = {"fasta": "", "names": "--names", "summary": "--summary", "conversionTable": "--conversion-table", "taxonomyTree": "--taxonomy-tree", "nameTable": "--name-table", "sizeTable": "--size-table"}
@@ -296,45 +296,100 @@ task DownloadTaxonomy {
task Kreport {
input {
- String? preCommand
- File centrifugeOut
- Boolean inputIsCompressed
- String outputDir
- String suffix = "kreport"
- String prefix = "centrifuge"
- String indexPrefix
- Boolean? onlyUnique ## removed in 1.0.4
- Boolean? showZeros
- Boolean? isCountTable
- Int? minScore
- Int? minLength
-
- Int cores = 1
+ File centrifugeClassification
+ String outputPrefix
+ Array[File]+ indexFiles
+ Boolean noLCA = false
+ Boolean showZeros = false
+ Boolean isCountTable = false
+
+ Int? minimumScore
+ Int? minimumLength
+
String memory = "4G"
+ String dockerImage = "quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5"
}
- String kreportFilePath = outputDir + "/" + prefix + "." + suffix
- command {
- set -e -o pipefail
- ~{preCommand}
+ command <<<
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ indexBasename="$(basename ~{sub(indexFiles[0], "\.[0-9]\.cf", "")})"
+ for file in ~{sep=" " indexFiles}
+ do
+ ln ${file} $PWD/"$(basename ${file})"
+ done
centrifuge-kreport \
- -x ~{indexPrefix} \
- ~{true="--only-unique" false="" onlyUnique} \
+ -x $PWD/${indexBasename} \
+ ~{true="--no-lca" false="" noLCA} \
~{true="--show-zeros" false="" showZeros} \
~{true="--is-count-table" false="" isCountTable} \
- ~{"--min-score " + minScore} \
- ~{"--min-length " + minLength} \
- ~{true="<(zcat" false="" inputIsCompressed} ~{centrifugeOut}\
- ~{true=")" false="" inputIsCompressed} \
- > ~{kreportFilePath}
+ ~{"--min-score " + minimumScore} \
+ ~{"--min-length " + minimumLength} \
+ ~{centrifugeClassification} \
+ > ~{outputPrefix + "_kreport.tsv"}
+ >>>
+
+ output {
+ File outputKreport = outputPrefix + "_kreport.tsv"
+ }
+
+ runtime {
+ memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ centrifugeClassification: {description: "File with Centrifuge classification results.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ indexFiles: {description: "The files of the index for the reference genomes.", category: "required"}
+ noLCA: {description: "Do not report the LCA of multiple assignments, but report count fractions at the taxa.", category: "advanced"}
+ showZeros: {description: "Show clades that have zero reads.", category: "advanced"}
+ isCountTable: {description: "The format of the file is taxID<tab>COUNT.", category: "advanced"}
+ minimumScore: {description: "Require a minimum score for reads to be counted.", category: "advanced"}
+ minimumLength: {description: "Require a minimum alignment length to the read.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ 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
+ outputKreport: {description: "File with kraken style report."}
+ }
+}
+
+task KTimportTaxonomy {
+ input {
+ File inputFile
+ String outputPrefix
+
+ String memory = "4G"
+ String dockerImage = "biocontainers/krona:v2.7.1_cv1"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPrefix})"
+ cat ~{inputFile} | cut -f 1,3 > kronaInput.krona
+ ktImportTaxonomy kronaInput.krona
+ cp taxonomy.krona.html ~{outputPrefix + "_krona.html"}
}
output {
- File kreport = kreportFilePath
+ File outputKronaPlot = outputPrefix + "_krona.html"
}
runtime {
- cpu: cores
memory: memory
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ # inputs
+ inputFile: {description: "File with Centrifuge classification results.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ outputKronaPlot: {description: "Krona taxonomy plot html file."}
}
}
diff --git a/gatk.wdl b/gatk.wdl
index eb050f9a197ec5c88bcbab857a49b119a6884ae4..ff17dadcff8286e6e8a6702fa3117f8722a9596a 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -723,15 +723,66 @@ task GatherBqsrReports {
}
}
+task GenomicsDBImport {
+ input {
+ Array[File] gvcfFiles
+ Array[File] gvcfFilesIndex
+ Array[File]+ intervals
+ String genomicsDBWorkspacePath = "genomics_db"
+ String genomicsDBTarFile = "genomics_db.tar.gz"
+ String? tmpDir
+ String memory = "12G"
+ String javaXmx = "4G"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{genomicsDBWorkspacePath})"
+ gatk --java-options -Xmx~{javaXmx} \
+ GenomicsDBImport \
+ -V ~{sep=" -V " gvcfFiles} \
+ --genomicsdb-workspace-path ~{genomicsDBWorkspacePath} \
+ ~{"--tmp-dir " + tmpDir} \
+ -L ~{sep=" -L " intervals}
+ bash -c 'tar -cvzf ~{genomicsDBTarFile} ~{genomicsDBWorkspacePath}/*'
+ }
+
+ output {
+ File genomicsDbTarArchive = genomicsDBTarFile
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ gvcfFiles: {description: "The gvcfFiles to be merged.", category: "required"}
+ gvcfFilesIndex: {description: "Indexes for the gvcfFiles.", category: "required"}
+ intervals: {description: "intervals over which to operate.", category: "required"}
+ genomicsDBWorkspacePath: {description: "Where the genomicsDB files should be stored", category: "advanced"}
+ genomicsDBTarFile: {description: "Where the .tar file containing the genomicsDB should be stored", category: "advanced"}
+ tmpDir: {description: "Alternate temporary directory in case there is not enough space. Must be mounted when using containers",
+ category: "advanced"}
+ 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"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
+}
+
task GenotypeGVCFs {
input {
- Array[File]+ gvcfFiles
- Array[File]+ gvcfFilesIndex
+ File gvcfFile
+ File gvcfFileIndex
Array[File]+ intervals
String outputPath
File referenceFasta
File referenceFastaDict
File referenceFastaFai
+ Array[String] annotationGroups = ["StandardAnnotation"]
File? dbsnpVCF
File? dbsnpVCFIndex
@@ -747,11 +798,10 @@ task GenotypeGVCFs {
GenotypeGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
- ~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpVCF} \
- -G StandardAnnotation \
+ ~{"-D " + dbsnpVCF} \
+ ~{true="-G" false="" length(annotationGroups) > 0} ~{sep=" -G " annotationGroups} \
--only-output-calls-starting-in-intervals \
- -new-qual \
- -V ~{sep=' -V ' gvcfFiles} \
+ -V ~{gvcfFile} \
-L ~{sep=' -L ' intervals}
}
@@ -767,8 +817,8 @@ task GenotypeGVCFs {
}
parameter_meta {
- gvcfFiles: {description: "The GVCF files to be genotypes.", category: "required"}
- gvcfFilesIndex: {description: "The index of the input GVCF files.", category: "required"}
+ gvcfFile: {description: "The GVCF file to be genotyped.", category: "required"}
+ gvcfFileIndex: {description: "The index of the input GVCF file.", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
outputPath: {description: "The location to write the output VCF file to.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
@@ -776,6 +826,7 @@ task GenotypeGVCFs {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ annotationGroups: {description: "Which annotation groups will be used for the annotation", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
@@ -839,20 +890,21 @@ task GetPileupSummaries {
}
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
-task HaplotypeCallerGvcf {
+task HaplotypeCaller {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
Array[File]+? intervalList
Array[File]+? excludeIntervalList
- String gvcfPath
+ String outputPath
File referenceFasta
File referenceFastaIndex
File referenceFastaDict
- Float contamination = 0.0
+ Float? contamination
File? dbsnpVCF
File? dbsnpVCFIndex
Int? ploidy
+ Boolean gvcf = false
String memory = "12G"
String javaXmx = "4G"
@@ -861,23 +913,23 @@ task HaplotypeCallerGvcf {
command {
set -e
- mkdir -p "$(dirname ~{gvcfPath})"
+ mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
HaplotypeCaller \
-R ~{referenceFasta} \
- -O ~{gvcfPath} \
+ -O ~{outputPath} \
-I ~{sep=" -I " inputBams} \
~{"--sample-ploidy " + ploidy} \
~{true="-L" false="" defined(intervalList)} ~{sep=' -L ' intervalList} \
~{true="-XL" false="" defined(excludeIntervalList)} ~{sep=' -XL ' excludeIntervalList} \
- ~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpVCF} \
- -contamination ~{contamination} \
- -ERC GVCF
+ ~{"-D" + dbsnpVCF} \
+ ~{"--contamination-fraction-per-sample-file " + contamination} \
+ ~{true="-ERC GVCF" false="" gvcf}
}
output {
- File outputGVCF = gvcfPath
- File outputGVCFIndex = gvcfPath + ".tbi"
+ File outputVCF = outputPath
+ File outputVCFIndex = outputPath + ".tbi"
}
runtime {
@@ -890,8 +942,9 @@ task HaplotypeCallerGvcf {
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
- gvcfPath: {description: "The location to write the output GVCF to.", category: "required"}
+ outputPath: {description: "The location to write the output to.", category: "required"}
ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
+ gvcf: {description: "Whether the output should be a gvcf", category: "common"}
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.",