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Commit d101e77c authored by JasperBoom's avatar JasperBoom
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Add last set of updates.

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.github/PULL_REQUEST_TEMPLATE.md
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### Checklist
- [ ] Pull request details were added to CHANGELOG.md
- [ ] Pull request details were added to CHANGELOG.md.
- [ ] `parameter_meta` for each task is up to date.
CHANGELOG.md
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......@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
+ Samtools: `Sort` task now has `threads` in runtime instead of `1`.
+ Picard: Add parameter_meta to `SortSam`.
+ pbmm2: Add parameter_meta for `sample`.
+ Centrifuge: Rename output in task `KReport` to `KrakenReport` to resolve
......@@ -20,6 +21,7 @@ version 5.0.0-dev
+ Bam2fastx: Add localisation of input files to Bam2Fasta task.
+ isoseq3: `cores` input has been renamed to `threads` to match tool naming.
+ CCS: `cores` input has been renamed to `threads` to match tool naming.
+ Add PacBio preprocessing specific tasks `mergePacBio` & `ccsChunks`.
+ CCS: Update CCS to version 5.
+ deepvariant: Add task for DeepVariant.
+ gatk: Make intervals optional for GenotypeGVCFs.
......
pacbio.wdl 0 → 100644
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version 1.0
# Copyright (c) 2020 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 mergePacBio {
input {
Array[File]+ reports
String mergedReport
String memory = "4G"
String dockerImage = "lumc/pacbio-merge:0.2"
}
command {
set -e
mkdir -p $(dirname ~{mergedReport})
pacbio_merge \
--reports ~{sep=" " reports} \
--json-output ~{mergedReport}
}
runtime {
memory: memory
docker: dockerImage
}
output {
File MergedReport = mergedReport
}
parameter_meta {
# inputs
reports: {description: "The PacBio report files to merge.", category: "required"}
mergedReport: {description: "The location the merged PacBio report file should be written to.", category: "common"}
memory: {description: "The amount of memory this job will use.", 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 ccsChunks {
input {
Int chunkCount
String memory = "4G"
String dockerImage = "python:3.7-slim"
}
command {
set -e
python <<CODE
for i in range(1, ~{chunkCount} + 1):
print(i, ~{chunkCount}, sep="/")
CODE
}
runtime {
memory: memory
docker: dockerImage
}
output {
Array[String] chunks = read_lines(stdout())
}
parameter_meta {
# inputs
chunkCount: {description: "The number of chunks to create.", category: "required"}
memory: {description: "The amount of memory this job will use.", 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"}
}
}
samtools.wdl
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......@@ -431,7 +431,7 @@ task Sort {
# outputs
outputBam: {description: "Sorted BAM file."}
outputBamIndex: {description "Sorted BAM file index."}
outputBamIndex: {description: "Sorted BAM file index."}
}
}
......
seqtk.wdl
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......@@ -24,11 +24,12 @@ task Sample {
input {
File sequenceFile
String outFilePath = "subsampledReads.fq.gz"
String? preCommand
Int? seed
Boolean twoPassMode = false
Float fractionOrNumber # when above 1.0 is the number of reads, otherwise it's a fraction
Float fractionOrNumber # When above 1.0 is the number of reads, otherwise it's a fraction.
Boolean zip = true
String? preCommand
Int? seed
}
command {
......@@ -47,4 +48,4 @@ task Sample {
output {
File subsampledReads = outFilePath
}
}
\ No newline at end of file
}
smoove.wdl
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version 1.0
# MIT License
#
# Copyright (c) 2020 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
......@@ -32,8 +30,8 @@ task Call {
String outputDir = "./smoove"
String memory = "15G"
String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
}
command {
......@@ -52,9 +50,8 @@ task Call {
runtime {
memory: memory
docker: dockerImage
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
......@@ -63,8 +60,8 @@ task Call {
bamIndex: {description: "The index of the bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference.", category: "required" }
outputDir: {description: "The location the output VCF file should be written.", category: "common"}
sample: {description: "The name of the sample.", category: "required"}
outputDir: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum duration (in minutes) the tool is allowed to run.", 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"}
......
somaticseq.wdl
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......@@ -22,17 +22,18 @@ version 1.0
task ParallelPaired {
input {
File? classifierSNV
File? classifierIndel
String outputDir
File referenceFasta
File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
File tumorBam
File tumorBamIndex
File normalBam
File normalBamIndex
File? classifierSNV
File? classifierIndel
File? inclusionRegion
File? exclusionRegion
File? mutect2VCF
File? varscanSNV
File? varscanIndel
......@@ -95,17 +96,18 @@ task ParallelPaired {
}
parameter_meta {
classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
# inputs
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
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: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanSNV: {description: "An SNV VCF as produced by varscan.", category: "advanced"}
varscanIndel: {description: "An indel VCF as produced by varscan.", category: "advanced"}
......@@ -118,11 +120,9 @@ task ParallelPaired {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -133,12 +133,13 @@ task ParallelPairedTrain {
String outputDir
File referenceFasta
File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
File tumorBam
File tumorBamIndex
File normalBam
File normalBamIndex
File? inclusionRegion
File? exclusionRegion
File? mutect2VCF
File? varscanSNV
File? varscanIndel
......@@ -200,17 +201,18 @@ task ParallelPairedTrain {
}
parameter_meta {
# inputs
truthSNV: {description: "A VCF of true SNVs.", category: "required"}
truthIndel: {description: "A VCF of true indels.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
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: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanSNV: {description: "An SNV VCF as produced by varscan.", category: "advanced"}
varscanIndel: {description: "An indel VCF as produced by varscan.", category: "advanced"}
......@@ -223,25 +225,24 @@ task ParallelPairedTrain {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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 ParallelSingle {
input {
File? classifierSNV
File? classifierIndel
File bam
File bamIndex
String outputDir
File referenceFasta
File referenceFastaFai
File? classifierSNV
File? classifierIndel
File? inclusionRegion
File? exclusionRegion
File bam
File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
......@@ -291,40 +292,40 @@ task ParallelSingle {
}
parameter_meta {
classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
# inputs
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The index for the input BAM file.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
classifierSNV: {description: "A somaticseq SNV classifier.", category: "common"}
classifierIndel: {description: "A somaticseq Indel classifier.", category: "common"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The index for the input BAM file.", category: "required"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanVCF: {description: "A VCF as produced by varscan.", category: "advanced"}
vardictVCF: {description: "A VCF as produced by vardict.", category: "advanced"}
lofreqVCF: {description: "A VCF as produced by lofreq.", category: "advanced"}
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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 ParallelSingleTrain {
input {
File bam
File bamIndex
File truthSNV
File truthIndel
String outputDir
File referenceFasta
File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
File bam
File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
......@@ -373,6 +374,9 @@ task ParallelSingleTrain {
}
parameter_meta {
# inputs
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The index for the input BAM file.", category: "required"}
truthSNV: {description: "A VCF of true SNVs.", category: "required"}
truthIndel: {description: "A VCF of true indels.", category: "required"}
outputDir: {description: "The directory to write the output to.", category: "common"}
......@@ -380,19 +384,15 @@ task ParallelSingleTrain {
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
inclusionRegion: {description: "A bed file describing regions to include.", category: "common"}
exclusionRegion: {description: "A bed file describing regions to exclude.", category: "common"}
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The index for the input BAM file.", category: "required"}
mutect2VCF: {description: "A VCF as produced by mutect2.", category: "advanced"}
varscanVCF: {description: "A VCF as produced by varscan.", category: "advanced"}
vardictVCF: {description: "A VCF as produced by vardict.", category: "advanced"}
lofreqVCF: {description: "A VCF as produced by lofreq.", category: "advanced"}
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -400,17 +400,16 @@ task ModifyStrelka {
input {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
String dockerImage = "lethalfang/somaticseq:3.1.0"
Int timeMinutes = 20
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
command {
set -e
/opt/somaticseq/vcfModifier/modify_Strelka.py \
-infile ~{strelkaVCF} \
-outfile "modified_strelka.vcf"
first_FORMAT_line_num=$(grep -n -m 1 '##FORMAT' "modified_strelka.vcf" | cut -d : -f 1)
sed "$first_FORMAT_line_num"'i##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' "modified_strelka.vcf" > ~{outputVCFName}
}
......@@ -425,10 +424,10 @@ task ModifyStrelka {
}
parameter_meta {
# inputs
strelkaVCF: {description: "A vcf file as produced by strelka.", category: "required"}
outputVCFName: {description: "The location the output VCF file should be written to.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
spades.wdl
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......@@ -22,10 +22,11 @@ version 1.0
task Spades {
input {
String outputDir
String? preCommand
File read1
File? read2
String outputDir
String? preCommand
File? interlacedReads
File? sangerReads
File? pacbioReads
......@@ -44,12 +45,13 @@ task Spades {
Boolean? disableGzipOutput
Boolean? disableRepeatResolution
File? dataset
Int threads = 1
Int memoryGb = 16
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
Int threads = 1
Int memoryGb = 16
}
command {
......@@ -100,4 +102,4 @@ task Spades {
cpu: threads
memory: "~{memoryGb}G"
}
}
\ No newline at end of file
}
star.wdl
+ 12
− 8
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......@@ -24,6 +24,7 @@ task GenomeGenerate {
input {
String genomeDir = "STAR_index"
File referenceFasta
File? referenceGtf
Int? sjdbOverhang
......@@ -61,8 +62,10 @@ task GenomeGenerate {
File? sjdbListFromGtfOut = "~{genomeDir}/sjdbList.fromGTF.out.tab"
File? sjdbListOut = "~{genomeDir}/sjdbList.out.tab"
File? transcriptInfo = "~{genomeDir}/transcriptInfo.tab"
Array[File] starIndex = select_all([chrLength, chrNameLength, chrName, chrStart, genome, genomeParameters,
sa, saIndex, exonGeTrInfo, exonInfo, geneInfo, sjdbInfo, sjdbListFromGtfOut,
Array[File] starIndex = select_all([chrLength, chrNameLength, chrName,
chrStart, genome, genomeParameters,
sa, saIndex, exonGeTrInfo, exonInfo,
geneInfo, sjdbInfo, sjdbListFromGtfOut,
sjdbListOut, transcriptInfo])
}
......@@ -74,16 +77,15 @@ task GenomeGenerate {
}
parameter_meta {
# inputs
genomeDir: {description:"The directory the STAR index should be written to.", categroy: "common"}
referenceFasta: {description: "The reference Fasta file.", category: "required"}
referenceGtf: {description: "The reference GTF file.", category: "common"}
sjdbOverhang: {description: "Equivalent to STAR's `--sjdbOverhang` option.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -95,6 +97,8 @@ task Star {
String outFileNamePrefix
String outSAMtype = "BAM SortedByCoordinate"
String readFilesCommand = "zcat"
Int outBAMcompression = 1
Int? outFilterScoreMin
Float? outFilterScoreMinOverLread
Int? outFilterMatchNmin
......@@ -103,7 +107,6 @@ task Star {
String? twopassMode = "Basic"
Array[String]? outSAMattrRGline
String? outSAMunmapped = "Within KeepPairs"
Int outBAMcompression = 1
Int? limitBAMsortRAM
Int runThreadN = 4
......@@ -119,7 +122,7 @@ task Star {
# So we solve it with an optional memory string and using select_first
# in the runtime section.
#TODO Could be extended for all possible output extensions
#TODO: Could be extended for all possible output extensions.
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
command {
......@@ -157,12 +160,14 @@ task Star {
}
parameter_meta {
# inputs
inputR1: {description: "The first-/single-end FastQ files.", category: "required"}
inputR2: {description: "The second-end FastQ files (in the same order as the first-end files).", category: "common"}
indexFiles: {description: "The star index files.", category: "required"}
outFileNamePrefix: {description: "The prefix for the output files. May include directories.", category: "required"}
outSAMtype: {description: "The type of alignment file to be produced. Currently only `BAM SortedByCoordinate` is supported.", category: "advanced"}
readFilesCommand: {description: "Equivalent to star's `--readFilesCommand` option.", category: "advanced"}
outBAMcompression: {description: "The compression level of the output BAM.", category: "advanced"}
outFilterScoreMin: {description: "Equivalent to star's `--outFilterScoreMin` option.", category: "advanced"}
outFilterScoreMinOverLread: {description: "Equivalent to star's `--outFilterScoreMinOverLread` option.", category: "advanced"}
outFilterMatchNmin: {description: "Equivalent to star's `--outFilterMatchNmin` option.", category: "advanced"}
......@@ -174,7 +179,6 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
outBAMcompression: {description: "The compression level of the output BAM.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
......
strelka.wdl
+ 17
− 17
View file @ d101e77c
......@@ -29,11 +29,12 @@ task Germline {
Array[File]+ indexes
File referenceFasta
File referenceFastaFai
File? callRegions
File? callRegionsIndex
Boolean exome = false
Boolean rna = false
File? callRegions
File? callRegionsIndex
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 90
......@@ -61,28 +62,27 @@ task Germline {
}
runtime {
docker: dockerImage
cpu: cores
time_minutes: timeMinutes
memory: "~{memoryGb}G"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
runDir: {description: "The directory to use as run/output directory.", category: "common"}
bams: {description: "The input BAM files.", category: "required"}
indexes: {description: "The indexes for the input BAM files.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
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"}
rna: {description: "Whether or not the data is from RNA sequencing.", 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"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -95,11 +95,12 @@ task Somatic {
File tumorBamIndex
File referenceFasta
File referenceFastaFai
Boolean exome = false
File? callRegions
File? callRegionsIndex
File? indelCandidatesVcf
File? indelCandidatesVcfIndex
Boolean exome = false
Int cores = 1
Int memoryGb = 4
......@@ -133,13 +134,14 @@ task Somatic {
}
runtime {
docker: dockerImage
cpu: cores
time_minutes: timeMinutes
memory: "~{memoryGb}G"
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
runDir: {description: "The directory to use as run/output directory.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "required"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "required"}
......@@ -147,17 +149,15 @@ task Somatic {
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
exome: {description: "Whether or not the data is from exome sequencing.", 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"}
indelCandidatesVcf: {description: "An indel candidates VCF file from manta.", category: "advanced"}
indelCandidatesVcfIndex: {description: "The index for the indel candidates VCF file.", category: "advanced"}
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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
meta {
......@@ -165,4 +165,4 @@ task Somatic {
exclude: ["doNotDefineThis"]
}
}
}
\ No newline at end of file
}
stringtie.wdl
+ 10
− 8
View file @ d101e77c
......@@ -24,9 +24,10 @@ task Stringtie {
input {
File bam
File bamIndex
File? referenceGtf
Boolean skipNovelTranscripts = false
String assembledTranscriptsFile
File? referenceGtf
Boolean? firstStranded
Boolean? secondStranded
String? geneAbundanceFile
......@@ -64,19 +65,19 @@ task Stringtie {
}
parameter_meta {
# inputs
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The input BAM file's index.", category: "required"}
referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
skipNovelTranscripts: {description: "Whether new transcripts should be assembled or not.", category: "common"}
assembledTranscriptsFile: {description: "Where the output of the assembly should be written.", category: "required"}
referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -84,13 +85,14 @@ task Merge {
input {
Array[File]+ gtfFiles
String outputGtfPath
Boolean keepMergedTranscriptsWithRetainedIntrons = false
File? guideGtf
Int? minimumLength
Float? minimumCoverage
Float? minimumFPKM
Float? minimumTPM
Float? minimumIsoformFraction
Boolean keepMergedTranscriptsWithRetainedIntrons = false
String? label
String memory = "10G"
......@@ -125,19 +127,19 @@ task Merge {
}
parameter_meta {
# inputs
gtfFiles: {description: "The GTF files produced by stringtie.", category: "required"}
outputGtfPath: {description: "Where the output should be written.", category: "required"}
keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
guideGtf: {description: "Equivalent to the -G option of 'stringtie --merge'.", category: "advanced"}
minimumLength: {description: "Equivalent to the -m option of 'stringtie --merge'.", category: "advanced"}
minimumCoverage: {description: "Equivalent to the -c option of 'stringtie --merge'.", category: "advanced"}
minimumFPKM: {description: "Equivalent to the -F option of 'stringtie --merge'.", category: "advanced"}
minimumTPM: {description: "Equivalent to the -T option of 'stringtie --merge'.", category: "advanced"}
minimumIsoformFraction: {description: "Equivalent to the -f option of 'stringtie --merge'.", category: "advanced"}
keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
label: {description: "Equivalent to the -l option of 'stringtie --merge'.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
survivor.wdl
+ 9
− 10
View file @ d101e77c
version 1.0
# MIT License
#
# Copyright (c) 2018 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
......@@ -32,6 +30,7 @@ task Merge {
Boolean distanceBySvSize = false
Int minSize = 30
String outputPath = "./survivor/merged.vcf"
String memory = "24G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
......@@ -64,15 +63,15 @@ task Merge {
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: "advanced"}
suppVecs: {description: "The minimum number of SV callers to support the merging", category: "advanced"}
svType: {description: "A boolean to include the type SV to be merged", category: "advanced"}
strandType: {description: "A boolean to include strand type of an SV to be merged", category: "advanced"}
distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size", category: "advanced"}
minSize: {description: "The mimimum size of SV to be merged", category: "advanced"}
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: "advanced"}
suppVecs: {description: "The minimum number of SV callers to support the merging.", category: "advanced"}
svType: {description: "A boolean to include the type SV to be merged.", category: "advanced"}
strandType: {description: "A boolean to include strand type of an SV to be merged.", category: "advanced"}
distanceBySvSize: {description: "A boolean to predict the pairwise distance between the SVs based on their size.", category: "advanced"}
minSize: {description: "The mimimum size of SV to be merged.", category: "advanced"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs", category: "advanced"}
memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
......
talon.wdl
+ 5
− 5
View file @ d101e77c
version 1.0
# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
# 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
......@@ -8,10 +8,10 @@ version 1.0
# 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 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
......
transcriptclean.wdl
+ 10
− 11
View file @ d101e77c
version 1.0
# Copyright (c) 2019 Sequencing Analysis Support Core - Leiden University Medical Center
# 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
......@@ -8,10 +8,10 @@ version 1.0
# 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 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
......@@ -54,10 +54,10 @@ task GetSJsFromGtf {
parameter_meta {
# inputs
gtfFile: {description: "Input gtf file", category: "required"}
genomeFile: {description: "Reference genome", category: "required"}
minIntronSize: {description: "Minimum size of intron to consider a junction.", category: "advanced"}
gtfFile: {description: "Input gtf file.", category: "required"}
genomeFile: {description: "Reference genome.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
minIntronSize: {description: "Minimum size of intron to consider a junction.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
......@@ -97,7 +97,7 @@ task GetTranscriptCleanStats {
parameter_meta {
# inputs
inputSam: {description: "Output sam file from transcriptclean", category: "required"}
inputSam: {description: "Output sam file from transcriptclean.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
......@@ -189,8 +189,7 @@ task TranscriptClean {
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
# outputs
fastaFile: {description: "Fasta file containing corrected reads."}
......
umi-tools.wdl
+ 21
− 20
View file @ d101e77c
version 1.0
# Copyright (c) 2017 Sequencing Analysis Support Core - Leiden University Medical Center
# Copyright (c) 2017 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
......@@ -8,10 +8,10 @@ version 1.0
# 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 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
......@@ -26,9 +26,10 @@ task Extract {
File? read2
String bcPattern
String? bcPattern2
Boolean threePrime = false
String read1Output = "umi_extracted_R1.fastq.gz"
String? read2Output = "umi_extracted_R2.fastq.gz"
Boolean threePrime = false
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
}
......@@ -50,21 +51,21 @@ task Extract {
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
read1: {description: "The first/single-end fastq file.", category: "required"}
read2: {description: "The second-end fastq file.", category: "common"}
bcPattern: {description: "The pattern to be used for UMI extraction. See the umi_tools docs for more information.", category: "required"}
bcPattern2: {description: "The pattern to be used for UMI extraction in the second-end reads. See the umi_tools docs for more information.", category: "advanced"}
threePrime: {description: "Whether or not the UMI's are at the reads' 3' end. If false the UMIs are extracted from the 5' end.", category: "advanced"}
read1Output: {description: "The location to write the first/single-end output fastq file to.", category: "advanced"}
read2Output: {description: "The location to write the second-end output fastq file to.", category: "advanced"}
threePrime: {description: "Whether or not the UMI's are at the reads' 3' end. If false the UMIs are extracted from the 5' end.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
......@@ -72,15 +73,15 @@ task Dedup {
input {
File inputBam
File inputBamIndex
String? umiSeparator
String outputBamPath
String? statsPrefix
Boolean paired = true
String? umiSeparator
String? statsPrefix
String memory = "25G"
Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30)
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9).
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
}
......@@ -107,21 +108,21 @@ task Dedup {
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
inputBam: {description: "The input BAM file.", categrory: "required"}
inputBamIndex: {description: "The index for the ipnut BAM file.", cateogry: "required"}
outputBamPath: {description: "The location to write the output BAM file to.", category: "required"}
statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
paired: {description: "Whether or not the data is paired.", category: "common"}
umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
memory: {description: "The amount of memory required for the task.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
unicycler.wdl
+ 3
− 2
View file @ d101e77c
......@@ -22,12 +22,13 @@ version 1.0
task Unicycler {
input {
String out
String? preCommand
File? short1
File? short2
File? unpaired
File? long
String out
Int? verbosity
Int? minFastaLength
Int? keep
......@@ -125,4 +126,4 @@ task Unicycler {
cpu: threads
memory: memory
}
}
\ No newline at end of file
}
vardict.wdl
+ 19
− 22
View file @ d101e77c
......@@ -27,29 +27,28 @@ task VarDict {
String tumorSampleName
File tumorBam
File tumorBamIndex
String? normalSampleName
File? normalBam
File? normalBamIndex
File referenceFasta
File referenceFastaFai
File bedFile
String outputVcf
Int chromosomeColumn = 1
Int startColumn = 2
Int endColumn = 3
Int geneColumn = 4
Boolean outputCandidateSomaticOnly = true
Boolean outputAllVariantsAtSamePosition = true
Float mappingQuality = 20
Int minimumTotalDepth = 8
Int minimumVariantDepth = 4
Float minimumAlleleFrequency = 0.02
Int chromosomeColumn = 1
Int startColumn = 2
Int endColumn = 3
Int geneColumn = 4
String? normalSampleName
File? normalBam
File? normalBamIndex
String javaXmx = "16G"
Int threads = 1
String memory = "18G"
String javaXmx = "16G"
Int timeMinutes = 300
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
}
......@@ -93,33 +92,31 @@ task VarDict {
}
parameter_meta {
# inputs
tumorSampleName: {description: "The name of the tumor/case sample.", category: "required"}
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"}
normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
bedFile: {description: "A bed file describing the regions to operate on. These regions must be below 1e6 bases in size.", category: "required"}
outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
outputCandidateSomaticOnly: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.", category: "advanced"}
outputAllVariantsAtSamePosition: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.", category: "advanced"}
mappingQuality: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.", category: "advanced"}
minimumTotalDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.", category: "advanced"}
minimumVariantDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.", category: "advanced"}
minimumAlleleFrequency: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.", category: "advanced"}
chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.", category: "advanced"}
threads: {description: "The number of threads to use.", 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"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
vt.wdl
+ 10
− 10
View file @ d101e77c
version 1.0
# Copyright (c) 2020 Sequencing Analysis Support Core - Leiden University Medical Center
# Copyright (c) 2020 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
......@@ -8,10 +8,10 @@ version 1.0
# 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 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
......@@ -28,9 +28,10 @@ task Normalize {
File referenceFastaFai
Boolean ignoreMaskedRef = false
String outputPath = "./vt/normalized_decomposed.vcf"
String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
String memory = "4G"
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
}
command {
......@@ -56,13 +57,12 @@ task Normalize {
# inputs
inputVCF: {description: "The VCF file to process.", category: "required"}
inputVCFIndex: {description: "The index of the VCF file to be processed.", category: "required"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
ignoreMaskedRef: {description: "Warns but does not exit when REF is inconsistent with masked reference sequence for non SNPs", category: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
ignoreMaskedRef: {description: "Warns but does not exit when REF is inconsistent with masked reference sequence for non SNPs.", category: "advanced"}
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
memory: {description: "The memory required to run the programs.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
}
}
whatshap.wdl
+ 58
− 53
View file @ d101e77c
......@@ -20,10 +20,14 @@ version 1.0
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task Phase {
input {
String outputVCF
File vcf
File vcfIndex
File phaseInput
File phaseInputIndex
File? reference
File? referenceIndex
String? tag
......@@ -33,20 +37,15 @@ task Phase {
String? chromosome
String? threshold
String? ped
File vcf
File vcfIndex
File phaseInput
File phaseInputIndex
String memory = "4G"
Int timeMinutes = 120
# Whatshap 1.0, tabix 0.2.5
# Whatshap 1.0, tabix 0.2.5.
String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
}
command {
set -e
whatshap phase \
~{vcf} \
~{phaseInput} \
......@@ -69,24 +68,27 @@ task Phase {
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
outputVCF: {description: "Output VCF file. Add .gz to the file name to get compressed output. If omitted, use standard output.", category: "common"}
reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created", category: "common"}
tag: {description: "Store phasing information with PS tag (standardized) or HP tag (used by GATK ReadBackedPhasing) (default: {description: PS)", category: "common"}
algorithm: {description: "Phasing algorithm to use (default: {description: whatshap)", category: "advanced"}
indels: {description: "Also phase indels (default: {description: do not phase indels)", category: "common"}
vcf: {description: "VCF or BCF file with variants to be phased (can be gzip-compressed).", category: "required"}
vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased.", category: "required"}
phaseInput: {description: "BAM, CRAM, VCF or BCF file(s) with phase information, either through sequencing reads (BAM, CRAM) or through phased blocks (VCF, BCF).", category: "required"}
phaseInputIndex: {description: "Index of BAM, CRAM, VCF or BCF file(s) with phase information.", category: "required"}
reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created.", category: "common"}
referenceIndex: {description: "Index of reference file.", category: "common"}
tag: {description: "Store phasing information with PS tag (standardized) or HP tag (used by GATK ReadBackedPhasing) (default: {description: PS).", category: "common"}
algorithm: {description: "Phasing algorithm to use (default: {description: whatshap).", category: "advanced"}
indels: {description: "Also phase indels (default: {description: do not phase indels).", category: "common"}
sample: {description: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times.", category: "common"}
chromosome: {description: "Name of chromosome to phase. If not given, all chromosomes in the input VCF are phased. Can be used multiple times.", category: "common"}
threshold: {description: "The threshold of the ratio between the probabilities that a pair of reads come from the same haplotype and different haplotypes in the read merging model (default: {description: 1000000).", category: "advanced"}
ped: {description: "Use pedigree information in PED file to improve phasing (switches to PedMEC algorithm). Columns 2, 3, 4 must refer to child, mother, and father sample names as used in the VCF and BAM/CRAM. Other columns are ignored.", category: "advanced"}
vcf: {description: "VCF or BCF file with variants to be phased (can be gzip-compressed)", category: "required"}
vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased", category: "required"}
phaseInput: {description: "BAM, CRAM, VCF or BCF file(s) with phase information, either through sequencing reads (BAM, CRAM) or through phased blocks (VCF, BCF)", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
......@@ -95,16 +97,17 @@ task Phase {
task Stats {
input {
File vcf
String? gtf
String? sample
String? tsv
String? blockList
String? chromosome
File vcf
String memory = "4G"
Int timeMinutes = 120
# Whatshap 1.0, tabix 0.2.5
# Whatshap 1.0, tabix 0.2.5.
String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
}
......@@ -125,18 +128,19 @@ task Stats {
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
gtf: "Write phased blocks to GTF file."
sample: "Name of the sample to process. If not given, use first sample found in VCF."
tsv: "Filename to write statistics to (tab-separated)."
blockList: "Filename to write list of all blocks to (one block per line)."
chromosome: "Name of chromosome to process. If not given, all chromosomes in the input VCF are considered."
vcf: "Phased VCF file"
# inputs
vcf: {description: "Phased VCF file.", category: "required"}
gtf: {description: "Write phased blocks to GTF file.", category: "common"}
sample: {description: "Name of the sample to process. If not given, use first sample found in VCF.", category: "common"}
tsv: {description: "Filename to write statistics to (tab-separated).", category: "common"}
blockList: {description: "Filename to write list of all blocks to (one block per line).", category: "advanced"}
chromosome: {description: "Name of chromosome to process. If not given, all chromosomes in the input VCF are considered.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
......@@ -145,57 +149,58 @@ task Stats {
task Haplotag {
input {
File vcf
File vcfIndex
File alignments
File alignmentsIndex
String outputFile
File? reference
File? referenceFastaIndex
String? regions
String? sample
File vcf
File vcfIndex
File alignments
File alignmentsIndex
String memory = "4G"
Int timeMinutes = 120
# Whatshap 1.0, tabix 0.2.5
# Whatshap 1.0, tabix 0.2.5.
String dockerImage = "quay.io/biocontainers/mulled-v2-5c61fe1d8c284dd05d26238ce877aa323205bf82:89b4005d04552bdd268e8af323df83357e968d83-0"
}
command {
set -e
whatshap haplotag \
~{vcf} \
~{alignments} \
~{if defined(outputFile) then ("--output " + '"' + outputFile+ '"') else ""} \
~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
~{if defined(regions) then ("--regions " + '"' + regions + '"') else ""} \
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""}
python3 -c "import pysam; pysam.index('~{outputFile}')"
~{vcf} \
~{alignments} \
~{if defined(outputFile) then ("--output " + '"' + outputFile+ '"') else ""} \
~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
~{if defined(regions) then ("--regions " + '"' + regions + '"') else ""} \
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""}
python3 -c "import pysam; pysam.index('~{outputFile}')"
}
output {
File bam = outputFile
File bamIndex = outputFile + ".bai"
File bam = outputFile
File bamIndex = outputFile + ".bai"
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
outputFile: "Output file. If omitted, use standard output."
reference: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created."
referenceFastaIndex: "Index for the reference file."
regions: "Specify region(s) of interest to limit the tagging to reads/variants overlapping those regions. You can specify a space-separated list of regions in the form of chrom:start-end, chrom (consider entire chromosome), or chrom:start (consider region from this start to end of chromosome)."
sample: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times."
vcf: "VCF file with phased variants (must be gzip-compressed and indexed)."
vcfIndex: "Index for the VCF or BCF file with variants to be phased."
alignments: "File (BAM/CRAM) with read alignments to be tagged by haplotype."
alignmentsIndex: "Index for the alignment file."
# inputs
vcf: {description: "VCF file with phased variants (must be gzip-compressed and indexed).", category: "required"}
vcfIndex: {description: "Index for the VCF or BCF file with variants to be phased.", category: "required"}
alignments: {description: "File (BAM/CRAM) with read alignments to be tagged by haplotype.", category: "required"}
alignmentsIndex: {description: "Index for the alignment file.", category: "required"}
outputFile: {description: "Output file. If omitted, use standard output.", category: "required"}
reference: {description: "Reference file. Provide this to detect alleles through re-alignment. If no index (.fai) exists, it will be created.", category: "common"}
referenceFastaIndex: {description: "Index for the reference file.", category: "common"}
regions: {description: "Specify region(s) of interest to limit the tagging to reads/variants overlapping those regions. You can specify a space-separated list of regions in the form of chrom:start-end, chrom (consider entire chromosome), or chrom:start (consider region from this start to end of chromosome).", category: "advanced"}
sample: {description: "Name of a sample to phase. If not given, all samples in the input VCF are phased. Can be used multiple times.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
......
wisestork.wdl
+ 25
− 19
View file @ d101e77c
......@@ -22,13 +22,15 @@ version 1.0
task Count {
input {
Int? binSize
File reference
File referenceIndex
File? binFile
File inputBam
File inputBamIndex
File reference
File referenceIndex
String outputBed = "output.bed"
Int? binSize
File? binFile
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -54,15 +56,17 @@ task Count {
task GcCorrect {
input {
Int? binSize
File reference
File referenceIndex
File? binFile
File inputBed
String outputBed = "output.bed"
Int? binSize
File? binFile
Float? fracN
Int? iter
Float? fracLowess
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -91,13 +95,16 @@ task GcCorrect {
task Newref {
input {
Int? binSize
File reference
File referenceIndex
File? binFile
Array[File]+ inputBeds
String outputBed = "output.bed"
Int? binSize
File? binFile
Int? nBins
Int memory = 2 + ceil(length(inputBeds) * 0.15)
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -106,36 +113,36 @@ task Newref {
mkdir -p $(dirname ~{outputBed})
wisestork newref \
~{"--binsize " + binSize} \
--reference ~{reference} \
~{"--bin-file " + binFile} \
--output ~{outputBed} \
-I ~{sep=" -I " inputBeds} \
~{"--n-bins " + nBins}
--reference ~{reference} \
~{"--bin-file " + binFile} \
--output ~{outputBed} \
-I ~{sep=" -I " inputBeds} \
~{"--n-bins " + nBins}
}
output {
File bedFile = outputBed
}
Int memory = 2 + ceil(length(inputBeds) * 0.15)
runtime {
docker: dockerImage
memory: "~{memory}G"
docker: dockerImage
}
}
task Zscore {
input {
Int? binSize
File reference
File referenceIndex
File? binFile
File inputBed
File inputBedIndex
File dictionaryFile
File dictionaryFileIndex
String outputBed = "output.bed"
Int? binSize
File? binFile
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -159,4 +166,3 @@ task Zscore {
docker: dockerImage
}
}
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