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Commit 1194e70c authored by Cats's avatar Cats
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Merge remote-tracking branch 'origin/develop' into CNV_calling

parents 85ceead3 94e54514
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CHANGELOG.md
+ 10
− 0
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......@@ -22,6 +22,16 @@ version 2.2.0-dev
+ PlotDenoisedCopyRatios
+ PlotModeledSegments
+ PreprocessIntervals
+ Add common.TextToFile task.
+ Add bedtools.Intersect.
+ Add `-o pipefail` to bedtools.MergeBedFiles to prevent errors in BED files
from going unnoticed.
+ Centrifuge: Fix -1/-U options for single end data.
+ Add bedtools.Complement, bedtools.Merge, and add a task to combine multiple
bed files called bedtools.MergeBedFiles. This task combines bedtools merge
and sort.
+ Change `g` parameter on bedtools.Sort to `genome`.
+ Add `ploidity` and `excludeIntervalList` to gatk.HaplotypeCallerGvcf.
+ Update centrifuge tasks.
+ Removed unused "cores" inputs from transcriptclean tasks.
+ Removed unused "cores" inputs from talon tasks.
......
bedtools.wdl
+ 154
− 3
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......@@ -20,6 +20,111 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task Complement {
input {
File faidx
File inputBed
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
String outputBed = basename(inputBed, "\.bed") + ".complement.bed"
}
# Use a fasta index file to get the genome sizes. And convert that to the
# bedtools specific "genome" format.
command {
set -e
cut -f1,2 ~{faidx} > sizes.genome
bedtools complement \
-g sizes.genome \
-i ~{inputBed} \
> ~{outputBed}
}
output {
File complementBed = outputBed
}
runtime {
docker: dockerImage
}
parameter_meta {
faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes",
category: "required"}
inputBed: {description: "The inputBed to complement",
category: "required"}
outputBed: {description: "The path to write the output to",
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 Merge {
input {
File inputBed
String outputBed = "merged.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
command {
bedtools merge -i ~{inputBed} > ~{outputBed}
}
output {
File mergedBed = outputBed
}
runtime {
docker: dockerImage
}
parameter_meta {
inputBed: {description: "The bed to merge",
category: "required"}
outputBed: {description: "The path to write the output to",
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"
}
}
}
# Use cat, bedtools sort and bedtools merge to merge bedfiles in a single task.
task MergeBedFiles {
input {
Array[File]+ bedFiles
String outputBed = "merged.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
# A sorted bed is needed for bedtools merge
command {
set -e -o pipefail
cat ~{sep=" " bedFiles} | bedtools sort | bedtools merge > ~{outputBed}
}
output {
File mergedBed = outputBed
}
runtime {
docker: dockerImage
}
parameter_meta {
bedFiles: {description: "The bed files to merge",
category: "required"}
outputBed: {description: "The path to write the output to",
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 Sort {
input {
File inputBed
......@@ -29,7 +134,7 @@ task Sort {
Boolean chrThenSizeD = false
Boolean chrThenScoreA = false
Boolean chrThenScoreD = false
File? g
File? genome
File? faidx
String outputBed = "output.sorted.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
......@@ -46,16 +151,62 @@ task Sort {
~{true="-chrThenSizeD" false="" chrThenSizeD} \
~{true="-chrThenScoreA" false="" chrThenScoreA} \
~{true="-chrThenScoreD" false="" chrThenScoreD} \
~{"-g " + g} \
~{"-g " + genome} \
~{"-faidx" + faidx} \
> ~{outputBed}
}
output {
File bedFile = outputBed
File sortedBed = outputBed
}
runtime {
docker: dockerImage
}
}
task Intersect {
input {
File regionsA
File regionsB
# Giving a faidx file will set the sorted option.
File? faidx
String outputBed = "intersect.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
Boolean sorted = defined(faidx)
command {
set -e
~{"cut -f1,2 " + faidx} ~{true="> sorted.genome" false ="" sorted}
bedtools intersect \
-a ~{regionsA} \
-b ~{regionsB} \
~{true="-sorted" false="" sorted} \
~{true="-g sorted.genome" false="" sorted} \
> ~{outputBed}
}
output {
File intersectedBed = outputBed
}
runtime {
docker: dockerImage
}
parameter_meta {
faidx: {description: "The fasta index (.fai) file that is used to create the genome file required for sorted output. Implies sorted option.",
category: "common"}
regionsA: {description: "Region file a to intersect",
category: "required"}
regionsB: {description: "Region file b to intersect",
category: "required"}
outputBed: {description: "The path to write the output to",
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"
}
}
}
centrifuge.wdl
+ 3
− 3
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......@@ -91,8 +91,8 @@ task Classify {
Array[File]+ read1
String outputPrefix
String outputName = basename(outputPrefix)
Array[File] read2 = []
Array[File]? read2
Int? trim5
Int? trim3
Int? reportMaxDistinct
......@@ -121,8 +121,8 @@ task Classify {
~{"--host-taxids " + hostTaxIDs} \
~{"--exclude-taxids " + excludeTaxIDs} \
~{"-x " + indexPrefix} \
~{true="-1 " false="-U " defined(read2)} ~{sep="," read1} \
~{"-2 "} ~{sep="," read2} \
~{true="-1" false="-U" length(read2) > 0} ~{sep="," read1} \
~{true="-2" false="" length(read2) > 0} ~{sep="," read2} \
~{"-S " + outputPrefix + "/" + outputName + "_classification.tsv"} \
~{"--report-file " + outputPrefix + "/" + outputName + "_output_report.tsv"}
}
......
common.wdl
+ 28
− 0
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......@@ -158,6 +158,34 @@ task StringArrayMd5 {
}
}
task TextToFile {
input {
String text
String outputFile = "out.txt"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
command <<<
echo $'~{text}' > ~{outputFile}
>>>
output {
File out = outputFile
}
parameter_meta {
text: {description: "The text to print", category: "required"}
outputFile: {description: "The name of the output file", category: "common"}
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"}
}
runtime {
memory: "1G"
docker: dockerImage
}
}
task YamlToJson {
input {
File yaml
......
gatk.wdl
+ 9
− 3
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......@@ -841,7 +841,8 @@ task HaplotypeCallerGvcf {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
Array[File]+ intervalList
Array[File]+? intervalList
Array[File]+? excludeIntervalList
String gvcfPath
File referenceFasta
File referenceFastaIndex
......@@ -849,6 +850,7 @@ task HaplotypeCallerGvcf {
Float contamination = 0.0
File? dbsnpVCF
File? dbsnpVCFIndex
Int? ploidy
String memory = "12G"
String javaXmx = "4G"
......@@ -863,7 +865,9 @@ task HaplotypeCallerGvcf {
-R ~{referenceFasta} \
-O ~{gvcfPath} \
-I ~{sep=" -I " inputBams} \
-L ~{sep=' -L ' intervalList} \
~{"--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
......@@ -882,8 +886,10 @@ task HaplotypeCallerGvcf {
parameter_meta {
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
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: "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"}
ploidy: {description: "The ploidy with which the variants should be called.", 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.",
......
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