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Commit bb0a7b9a authored by JasperBoom's avatar JasperBoom
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Reorder some stuff

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clever.wdl
+ 29
− 26
View file @ bb0a7b9a
version 1.0
version 1.0
import "bwa.wdl"
task Prediction {
input {
File bamFile
File bamIndex
BwaIndex bwaIndex
String outputPath
Int threads = 10
String outputPath
Int threads = 10
String memory = "15G"
String dockerImage = "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
}
command {
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
clever \
......@@ -22,27 +25,27 @@ task Prediction {
~{bamFile} \
~{bwaIndex.fastaFile} \
~{outputPath}
}
}
output {
File predictions = outputPath + "/predictions.vcf"
}
}
runtime {
cpu: threads
memory: memory
docker: dockerImage
}
}
parameter_meta {
# inputs
bamFile: {description: "The bam file to process.", category: "required"}
bamIndex: {description: "The index bam file.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", 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"}
bwaIndex: {description: "The BWA index files.", category: "required"}
memory: {description: "The memory required to run the programs", category: "common"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "common"}
memory: {description: "The memory required to run the programs", 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"}
}
}
......@@ -53,11 +56,12 @@ task Mateclever {
BwaIndex bwaIndex
File predictions
String outputPath
Int threads = 10
String memory = "15G"
Int cleverMaxDelLength = 100000
Int maxLengthDiff= 30
Int maxOffset = 150
Int maxOffset = 150
Int threads = 10
String memory = "15G"
String dockerImage = "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
}
......@@ -76,26 +80,25 @@ task Mateclever {
predictions.list \
~{outputPath}
}
output {
File matecleverVcf = outputPath + "/deletions.vcf"
File matecleverVcf = outputPath + "/deletions.vcf"
}
runtime {
cpu: threads
memory: memory
docker: dockerImage
docker: dockerImage
}
parameter_meta {
fiteredBam: {description: "The bam file where sequences less than 30bp were removed.", category: "required"}
indexedFiteredBam: {description: "The index of the filtered bam file.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", 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"}
bwaIndex: {description: "The BWA index files.", category: "required"}
predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"}
memory: {description: "The memory required to run the programs", category: "common"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "common"}
memory: {description: "The memory required to run the programs", 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"}
}
}
delly.wdl
+ 6
− 6
View file @ bb0a7b9a
......@@ -8,11 +8,12 @@ task CallSV {
File bamIndex
File referenceFasta
File referenceFastaFai
String outputPath
String outputPath
String memory = "15G"
String dockerImage = "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
......@@ -25,10 +26,10 @@ task CallSV {
output {
File dellyBcf = outputPath
}
runtime {
docker: dockerImage
memory: memory
docker: dockerImage
}
parameter_meta {
......@@ -37,8 +38,7 @@ task CallSV {
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
outputPath: {description: "The location the output VCF file should be written.", 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"}
memory: {description: "The memory required to run the programs", 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"}
}
}
manta.wdl
+ 9
− 11
View file @ bb0a7b9a
......@@ -57,6 +57,7 @@ task Somatic {
}
parameter_meta {
# inputs
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
......@@ -67,17 +68,14 @@ task Somatic {
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", 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"}
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 Germline {
input {
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
File bamFile
File bamIndex
File referenceFasta
......@@ -86,9 +84,10 @@ task Germline {
File? callRegions
File? callRegionsIndex
Boolean exome = false
Int cores = 1
Int memoryGb = 4
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
command {
......@@ -99,7 +98,7 @@ task Germline {
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
......@@ -110,7 +109,7 @@ task Germline {
File mantaVCF = runDir + "/results/variants/diploidSV.vcf.gz"
File mantaVCFindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
runtime {
cpu: cores
memory: "~{memoryGb}G"
......@@ -118,18 +117,17 @@ task Germline {
}
parameter_meta {
runDir: {description: "The directory to use as run/output directory.", category: "common"}
bamFile: {description: "The bam file to process.", category: "required"}
bamIndex: {description: "The index bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
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"}
runDir: {description: "The directory to use as run/output directory.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
memoryGb: {description: "The memory required to run the manta", category: "common"}
cores: {description: "The the number of cores required to run a program", category: "common"}
memoryGb: {description: "The memory required to run the manta", 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"}
}
}
picard.wdl
+ 15
− 6
View file @ bb0a7b9a
......@@ -33,6 +33,7 @@ task BedToIntervalList {
}
parameter_meta {
# inputs
bedFile: {description: "A bed file.", category: "required"}
dict: {description: "A sequence dict file.", category: "required"}
outputPath: {description: "The location the output interval list should be written to.",
......@@ -138,6 +139,7 @@ task CollectMultipleMetrics {
}
parameter_meta {
# inputs
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
......@@ -209,6 +211,7 @@ task CollectRnaSeqMetrics {
}
parameter_meta {
# inputs
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
......@@ -268,6 +271,7 @@ task CollectTargetedPcrMetrics {
}
parameter_meta {
# inputs
inputBam: {description: "The input BAM file for which metrics will be collected.",
category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
......@@ -326,6 +330,7 @@ task GatherBamFiles {
}
parameter_meta {
# inputs
inputBams: {description: "The BAM files to be merged together.", category: "required"}
inputBamsIndex: {description: "The indexes of the input BAM files.", category: "required"}
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
......@@ -368,6 +373,7 @@ task GatherVcfs {
}
parameter_meta {
# inputs
inputVcfs: {description: "The VCF files to be merged together.", category: "required"}
inputVcfIndexes: {description: "The indexes of the input VCF files.", category: "required"}
outputVcfPath: {description: "The path where the merged VCF file will be written.", caregory: "required"}
......@@ -434,6 +440,7 @@ task MarkDuplicates {
}
parameter_meta {
# inputs
inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
inputBamIndexes: {description: "Th eindexes for the input BAM files.", category: "required"}
outputBamPath: {description: "The location where the ouptut BAM file should be written.", category: "required"}
......@@ -483,6 +490,7 @@ task MergeVCFs {
}
parameter_meta {
# inputs
inputVCFs: {description: "The VCF files to be merged.", category: "required"}
inputVCFsIndexes: {description: "The indexes of the VCF files.", category: "required"}
outputVcfPath: {description: "The location the output VCF file should be written to.", category: "required"}
......@@ -600,6 +608,7 @@ task SortVcf {
}
parameter_meta {
# inputs
vcfFiles: {description: "The VCF files to merge and sort.", category: "required"}
outputVcfPath: {description: "The location the sorted VCF files should be written to.", category: "required"}
dict: {description: "A sequence dictionary matching the VCF files.", category: "advanced"}
......@@ -614,12 +623,13 @@ task SortVcf {
task RenameSample {
input {
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
File inputVcf
String outputPath
String newSampleName
String memory = "24G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
}
command {
......@@ -642,13 +652,12 @@ task RenameSample {
}
parameter_meta {
# inputs
inputVcf: {description: "The VCF file to process.", category: "required"}
newSampleName: {description: "A string to replace the old sample name.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", 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"}
javaXmx: {description: "The max. memory allocated for JAVA", category: "common"}
newSampleName: {description: "A string to replace the old sample name.", category: "required"}
memory: {description: "The memory required to run the programs", category: "common"}
javaXmx: {description: "The max. memory allocated for JAVA", 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"}
}
}
samtools.wdl
+ 10
− 0
View file @ bb0a7b9a
......@@ -28,6 +28,7 @@ task BgzipAndIndex {
}
parameter_meta {
# inputs
inputFile: {description: "The file to be compressed and indexed.", category: "required"}
outputDir: {description: "The directory in which the output will be placed.", category: "required"}
type: {description: "The type of file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
......@@ -70,6 +71,7 @@ task Index {
}
parameter_meta {
# inputs
bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
category: "common"}
......@@ -105,6 +107,7 @@ task Merge {
}
parameter_meta {
# inputs
bamFiles: {description: "The BAM files to merge.", category: "required"}
outputBamPath: {description: "The location the merged BAM file should be written to.", category: "common"}
force: {description: "Equivalent to samtools merge's `-f` flag.", category: "advanced"}
......@@ -136,6 +139,7 @@ task SortByName {
}
parameter_meta {
# inputs
bamFile: {description: "The BAM file to get sorted.", category: "required"}
outputBamPath: {description: "The location the sorted BAM file should be written to.", 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.",
......@@ -166,6 +170,7 @@ task Markdup {
}
parameter_meta {
# inputs
inputBam: {description: "The BAM file to be processed.", category: "required"}
outputBamPath: {description: "The location of the output BAM file.", category: "required"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
......@@ -196,6 +201,7 @@ task Flagstat {
}
parameter_meta {
# inputs
inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
outputPath: {description: "The location the ouput should be written to.", category: "required"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
......@@ -249,6 +255,7 @@ task Fastq {
}
parameter_meta {
# inputs
inputBam: {description: "The bam file to process.", category: "required"}
outputRead1: {description: "The location the reads (first reads for pairs, in case of paired-end sequencing) should be written to.", category: "required"}
outputRead2: {description: "The location the second reads from pairs should be written to.", category: "common"}
......@@ -293,6 +300,7 @@ task Tabix {
}
parameter_meta {
# inputs
inputFile: {description: "The file to be indexed.", category: "required"}
outputFilePath: {description: "The location where the file should be written to. The index will appear alongside this link to the file.",
category: "common"}
......@@ -351,6 +359,7 @@ task View {
}
parameter_meta {
# inputs
inFile: {description: "A BAM, SAM or CRAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
outputFileName: {description: "The location the output BAM file should be written.", category: "common"}
......@@ -372,6 +381,7 @@ task FilterShortReadsBam {
File bamFile
String outputPathBam
String outputPathBamIndex
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
......
survivor.wdl
+ 14
− 13
View file @ bb0a7b9a
......@@ -4,7 +4,6 @@ import "common.wdl"
task Merge {
input{
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
Array[File] filePaths
Int breakpointDistance = 1000
Int suppVecs = 2
......@@ -14,10 +13,12 @@ task Merge {
Int minSize = 30
String sample
String outputPath
String memory = "128G"
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
}
command {
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
echo '~{sep="\n" filePaths}' > fileList
......@@ -30,29 +31,29 @@ task Merge {
~{distanceBySvSize} \
~{minSize} \
~{outputPath}
}
}
output {
File mergedVcf = outputPath
}
runtime {
docker: dockerImage
memory: memory
docker: dockerImage
}
parameter_meta {
# inputs
filePaths: {description: "An array of VCF files (predictions) to be merged by SURVIVOR", category: "required"}
breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "required"}
suppVecs: {description: "The minimum number of SV callers to support the merging", category: "required"}
svType: {description: "A boolean to include the type SV to be merged", category: "required"}
strandType: {description: "A boolean to include strand type of an SV to be merged", category: "required"}
distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "required"}
minSize: {description: "The mimimum size of SV to be merged", category: "required"}
sample: {description: "The name of the sample", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", 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"}
minSize: {description: "The mimimum size of SV to be merged", category: "required"}
distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "required"}
strandType: {description: "A boolean to include strand type of an SV to be merged", category: "required"}
svType: {description: "A boolean to include the type SV to be merged", category: "required"}
suppVecs: {description: "The minimum number of SV callers to support the merging", category: "required"}
breakpointDistance: {description: "The distance between pairwise breakpoints between SVs", category: "required"}
memory: {description: "The memory required to run the programs", 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"}
}
}
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