diff --git a/bcftools.wdl b/bcftools.wdl
index 8fa3fc3755a6e9bb5fe570b0543418c11ce139c2..fbc3639dfde586e2239d7bc22548046f7bdd4fbf 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -4,19 +4,20 @@ task Bcf2Vcf {
input {
File bcf
String outputPath
+
String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
}
-
+
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
bcftools view ~{bcf} -O v -o ~{outputPath}
}
-
+
output {
File outputVcf = outputPath
}
-
+
runtime {
docker: dockerImage
}
diff --git a/clever.wdl b/clever.wdl
index 57259074d4e35ea834660640ca6f159ea927fda7..4a0ba84b070334e631c95d6666b2104a7cb65e47 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -2,13 +2,17 @@ version 1.0
import "bwa.wdl"
-task Prediction {
+task Mateclever {
input {
- File bamFile
- File bamIndex
+ File fiteredBam
+ File indexedFiteredBam
BwaIndex bwaIndex
+ File predictions
String outputPath
-
+ Int cleverMaxDelLength = 100000
+ Int maxLengthDiff= 30
+ Int maxOffset = 150
+
Int threads = 10
String memory = "15G"
String dockerImage = "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
@@ -17,18 +21,21 @@ task Prediction {
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- clever \
+ echo ~{outputPath} ~{fiteredBam} ~{predictions} none > predictions.list
+ mateclever \
-T ~{threads} \
- --use_mapq \
- --sorted \
+ -k \
-f \
- ~{bamFile} \
+ -M ~{cleverMaxDelLength} \
+ -z ~{maxLengthDiff} \
+ -o ~{maxOffset} \
~{bwaIndex.fastaFile} \
+ predictions.list \
~{outputPath}
}
output {
- File predictions = outputPath + "/predictions.vcf"
+ File matecleverVcf = outputPath + "/deletions.vcf"
}
runtime {
@@ -39,26 +46,26 @@ task Prediction {
parameter_meta {
# inputs
- bamFile: {description: "The bam file to process.", category: "required"}
- bamIndex: {description: "The index bam file.", category: "required"}
+ 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"}
bwaIndex: {description: "The BWA index files.", category: "required"}
+ predictions: {description: "The predicted deletions (VCF) from clever.", category: "required"}
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: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+ cleverMaxDelLength: {description: "Maximum deletion length to look for from clever predictions.", category: "advanced"}
+ maxLengthDiff: {description: "Maximum length difference between split-read and read-pair deletion to be considered identical ", category: "advanced"}
+ maxOffset: {description: "Maximum center distance between split-read and read-pair deletion to be considered identical", 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 Mateclever {
+task Prediction {
input {
- File fiteredBam
- File indexedFiteredBam
+ File bamFile
+ File bamIndex
BwaIndex bwaIndex
- File predictions
String outputPath
- Int cleverMaxDelLength = 100000
- Int maxLengthDiff= 30
- Int maxOffset = 150
Int threads = 10
String memory = "15G"
@@ -68,21 +75,18 @@ task Mateclever {
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
- echo ~{outputPath} ~{fiteredBam} ~{predictions} none > predictions.list
- mateclever \
+ clever \
-T ~{threads} \
- -k \
+ --use_mapq \
+ --sorted \
-f \
- -M ~{cleverMaxDelLength} \
- -z ~{maxLengthDiff} \
- -o ~{maxOffset} \
+ ~{bamFile} \
~{bwaIndex.fastaFile} \
- predictions.list \
~{outputPath}
}
output {
- File matecleverVcf = outputPath + "/deletions.vcf"
+ File predictions = outputPath + "/predictions.vcf"
}
runtime {
@@ -92,6 +96,7 @@ task Mateclever {
}
parameter_meta {
+<<<<<<< HEAD
fiteredBam: {description: "The bam file where sequences less than 30bp were removed.", category: "advanced"}
indexedFiteredBam: {description: "The index of the filtered bam file.", category: "advanced"}
bwaIndex: {description: "The BWA index files.", category: "required"}
@@ -102,6 +107,15 @@ task Mateclever {
maxLengthDiff: {description: "Maximum length difference between split-read and read-pair deletion to be considered identical ", category: "advanced"}
cleverMaxDelLength: {description: "Maximum deletion length to look for from clever predictions.", category: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
+=======
+ # inputs
+ bamFile: {description: "The bam file to process.", category: "required"}
+ bamIndex: {description: "The index bam file.", category: "required"}
+ bwaIndex: {description: "The BWA index files.", category: "required"}
+ 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"}
+>>>>>>> 338f85339b62da7921f2d5d68d0870e81a80d542
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"}
}
}
diff --git a/delly.wdl b/delly.wdl
index f194bdcf6b6b50f7f9351c90be4b7192bffe16ff..33c5784ded5aa062a807726477db528af3c91420 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -33,6 +33,7 @@ task CallSV {
}
parameter_meta {
+ # inputs
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: "required"}
diff --git a/manta.wdl b/manta.wdl
index 3e9be16e56bf8cb98ded4903396ef19ae5b34728..055f7a7e40c99654c0ce2c635811e5bb31e1580b 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -2,15 +2,13 @@ version 1.0
import "common.wdl"
-task Somatic {
+task Germline {
input {
- File tumorBam
- File tumorBamIndex
- File? normalBam
- File? normalBamIndex
+ File bamFile
+ File bamIndex
File referenceFasta
File referenceFastaFai
- String runDir = "./manta_run"
+ String runDir
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -21,9 +19,9 @@ task Somatic {
}
command {
+ set -e
configManta.py \
- ~{"--normalBam " + normalBam} \
- ~{"--tumorBam " + tumorBam} \
+ ~{"--normalBam " + bamFile} \
--referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
@@ -36,18 +34,8 @@ task Somatic {
}
output {
- File candidateSmallIndelsVcf = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
- File candidateSmallIndelsVcfIndex = runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
- File candidateSVVcf = runDir + "/results/variants/candidateSV.vcf.gz"
- File candidatSVVcfIndex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
- File tumorSVVcf = if defined(normalBam)
- then runDir + "/results/variants/somaticSV.vcf.gz"
- else runDir + "/results/variants/tumorSV.vcf.gz"
- File tumorSVVcfIndex = if defined(normalBam)
- then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
- else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
- File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
- File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
+ File mantaVCF = runDir + "/results/variants/diploidSV.vcf.gz"
+ File mantaVCFindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
runtime {
@@ -58,29 +46,29 @@ 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"}
- normalBamIndex: {description: "The index for the normal/control sample's BAM file.", 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"}
+ 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" }
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"}
- cores: {description: "The number of cores to use.", category: "advanced"}
- memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
+ 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"}
}
}
-task Germline {
+task Somatic {
input {
- File bamFile
- File bamIndex
+ File tumorBam
+ File tumorBamIndex
+ File? normalBam
+ File? normalBamIndex
File referenceFasta
File referenceFastaFai
- String runDir
+ String runDir = "./manta_run"
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -91,9 +79,9 @@ task Germline {
}
command {
- set -e
configManta.py \
- ~{"--normalBam " + bamFile} \
+ ~{"--normalBam " + normalBam} \
+ ~{"--tumorBam " + tumorBam} \
--referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
@@ -106,8 +94,18 @@ task Germline {
}
output {
- File mantaVCF = runDir + "/results/variants/diploidSV.vcf.gz"
- File mantaVCFindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
+ File candidateSmallIndelsVcf = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
+ File candidateSmallIndelsVcfIndex = runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+ File candidateSVVcf = runDir + "/results/variants/candidateSV.vcf.gz"
+ File candidatSVVcfIndex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+ File tumorSVVcf = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz"
+ else runDir + "/results/variants/tumorSV.vcf.gz"
+ File tumorSVVcfIndex = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
+ else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
+ File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
+ File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
runtime {
@@ -130,4 +128,3 @@ task Germline {
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"}
}
}
-