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Commit 589712ab authored by JasperBoom's avatar JasperBoom
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Merge branch 'develop' of https://github.com/biowdl/tasks into BIOWDL-380

parents 4255eca7 7f1545f4
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star.wdl
+ 19
− 1
View file @ 589712ab
......@@ -19,7 +19,7 @@ task Star {
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
#TODO Needs to 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 {
......@@ -48,6 +48,24 @@ task Star {
memory: memory
docker: dockerImage
}
parameter_meta {
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"}
outStd: {description: "Equivalent to star's `--outStd` option.", category: "advanced"}
twopassMode: {description: "Equivalent to star's `--twopassMode` option.", category: "advanced"}
outSAMattrRGline: {description: "The readgroup lines for the fastq pairs given (in the same order as the fastq files).", category: "common"}
outSAMunmapped: {description: "Equivalent to star's `--outSAMunmapped` option.", category: "advanced"}
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"}
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 MakeStarRGline {
......
strelka.wdl
+ 43
− 0
View file @ 589712ab
......@@ -44,6 +44,23 @@ task Germline {
cpu: cores
memory: "~{memoryGb}G"
}
parameter_meta {
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"}
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"}
}
}
task Somatic {
......@@ -96,4 +113,30 @@ task Somatic {
cpu: cores
memory: "~{memoryGb}G"
}
parameter_meta {
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"}
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"}
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"}
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"}
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 {
WDL_AID: {
exclude: ["doNotDefineThis"]
}
}
}
\ No newline at end of file
talon.wdl
+ 95
− 218
View file @ 589712ab
......@@ -30,7 +30,6 @@ task CreateAbundanceFileFromDatabase {
File? whitelistFile
File? datasetsFile
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -52,40 +51,25 @@ task CreateAbundanceFileFromDatabase {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
databaseFile: {
description: "TALON database.",
category: "required"
}
annotationVersion: {
description: "Which annotation version to use.",
category: "required"
}
genomeBuild: {
description: "Genome build to use.",
category: "required"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
whitelistFile: {
description: "Whitelist file of transcripts to include in the output.",
category: "advanced"
}
datasetsFile: {
description: "A file indicating which datasets should be included.",
category: "advanced"
}
outputAbundanceFile: {
description: "Abundance for each transcript in the TALON database across datasets.",
category: "required"
}
# inputs
databaseFile: {description: "TALON database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetsFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputAbundanceFile: {description: "Abundance for each transcript in the TALON database across datasets."}
}
}
......@@ -100,7 +84,6 @@ task CreateGtfFromDatabase {
File? whitelistFile
File? datasetFile
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -123,44 +106,25 @@ task CreateGtfFromDatabase {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
databaseFile: {
description: "TALON database.",
category: "required"
}
genomeBuild: {
description: "Genome build to use.",
category: "required"
}
annotationVersion: {
description: "Which annotation version to use.",
category: "required"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
observedInDataset: {
description: "The output will only include transcripts that were observed at least once.",
category: "advanced"
}
whitelistFile: {
description: "Whitelist file of transcripts to include in the output.",
category: "advanced"
}
datasetFile: {
description: "A file indicating which datasets should be included.",
category: "advanced"
}
outputGTFfile: {
description: "The genes, transcripts, and exons stored a TALON database in GTF format.",
category: "required"
}
# inputs
databaseFile: {description: "TALON database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
observedInDataset: {description: "The output will only include transcripts that were observed at least once.", category: "advanced"}
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputGTFfile: {description: "The genes, transcripts, and exons stored a TALON database in GTF format."}
}
}
......@@ -172,7 +136,6 @@ task FilterTalonTranscripts {
File? pairingsFile
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -192,28 +155,18 @@ task FilterTalonTranscripts {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
databaseFile: {
description: "TALON database.",
category: "required"
}
annotationVersion: {
description: "Which annotation version to use.",
category: "required"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
pairingsFile: {
description: "A file indicating which datasets should be considered together.",
category: "advanced"
}
databaseFile: {description: "TALON database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
pairingsFile: {description: "A file indicating which datasets should be considered together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
......@@ -225,7 +178,6 @@ task GetReadAnnotations {
File? datasetFile
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -245,32 +197,22 @@ task GetReadAnnotations {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
databaseFile: {
description: "TALON database.",
category: "required"
}
genomeBuild: {
description: "Genome build to use.",
category: "required"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
datasetFile: {
description: "A file indicating which datasets should be included.",
category: "advanced"
}
outputAnnotation: {
description: "Read-specific annotation information from a TALON database.",
category: "required"
}
# inputs
databaseFile: { description: "TALON database.", category: "required"}
genomeBuild: {description: "Genome build to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputAnnotation: {description: "Read-specific annotation information from a TALON database."}
}
}
......@@ -285,7 +227,6 @@ task InitializeTalonDatabase {
Int cutoff3p = 300
String outputPrefix
Int cores = 1
String memory = "10G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -309,48 +250,26 @@ task InitializeTalonDatabase {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
GTFfile: {
description: "GTF annotation containing genes, transcripts, and edges.",
category: "required"
}
genomeBuild: {
description: "Name of genome build that the GTF file is based on (ie hg38).",
category: "required"
}
annotationVersion: {
description: "Name of supplied annotation (will be used to label data).",
category: "required"
}
minimumLength: {
description: "Minimum required transcript length.",
category: "common"
}
novelIDprefix: {
description: "Prefix for naming novel discoveries in eventual TALON runs.",
category: "common"
}
cutoff5p: {
description: "Maximum allowable distance (bp) at the 5' end during annotation.",
category: "advanced"
}
cutoff3p: {
description: "Maximum allowable distance (bp) at the 3' end during annotation.",
category: "advanced"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
outputDatabase: {
description: "TALON database.",
category: "required"
}
# inputs
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"}
genomeBuild: {description: "Name of genome build that the GTF file is based on (ie hg38).", category: "required"}
annotationVersion: {description: "Name of supplied annotation (will be used to label data).", category: "required"}
minimumLength: { description: "Minimum required transcript length.", category: "common"}
novelIDprefix: {description: "Prefix for naming novel discoveries in eventual TALON runs.", category: "common"}
cutoff5p: { description: "Maximum allowable distance (bp) at the 5' end during annotation.", category: "advanced"}
cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputDatabase: {description: "TALON database."}
}
}
......@@ -358,7 +277,6 @@ task ReformatGtf {
input {
File GTFfile
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -374,16 +292,15 @@ task ReformatGtf {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
GTFfile: {
description: "GTF annotation containing genes, transcripts, and edges.",
category: "required"
}
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
......@@ -395,7 +312,6 @@ task SummarizeDatasets {
File? datasetGroupsCSV
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.4.1_cv1"
}
......@@ -415,32 +331,22 @@ task SummarizeDatasets {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
databaseFile: {
description: "TALON database.",
category: "required"
}
setVerbose: {
description: "Print out the counts in terminal.",
category: "advanced"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
datasetGroupsCSV: {
description: "File of comma-delimited dataset groups to process together.",
category: "advanced"
}
outputSummaryFile: {
description: "Tab-delimited file of gene and transcript counts for each dataset.",
category: "required"
}
# inputs
databaseFile: {description: "TALON database.", category: "required"}
setVerbose: {description: "Print out the counts in terminal.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputSummaryFile: {description: "Tab-delimited file of gene and transcript counts for each dataset."}
}
}
......@@ -496,53 +402,24 @@ task Talon {
}
parameter_meta {
SAMfiles: {
description: "Input SAM files.",
category: "required"
}
organism: {
description: "The name of the organism from which the samples originated.",
category: "required"
}
sequencingPlatform: {
description: "The sequencing platform used to generate long reads.",
category: "required"
}
databaseFile: {
description: "TALON database. Created using initialize_talon_database.py.",
category: "required"
}
genomeBuild: {
description: "Genome build (i.e. hg38) to use.",
category: "required"
}
minimumCoverage: {
description: "Minimum alignment coverage in order to use a SAM entry.",
category: "common"
}
minimumIdentity: {
description: "Minimum alignment identity in order to use a SAM entry.",
category: "common"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
outputUpdatedDatabase: {
description: "Updated TALON database.",
category: "required"
}
outputLog: {
description: "Log file from TALON run.",
category: "required"
}
outputAnnot: {
description: "Read annotation file from TALON run.",
category: "required"
}
outputConfigFile: {
description: "The TALON configuration file.",
category: "required"
}
# inputs
SAMfiles: {description: "Input SAM files.", category: "required"}
organism: {description: "The name of the organism from which the samples originated.", category: "required"}
sequencingPlatform: {description: "The sequencing platform used to generate long reads.", category: "required"}
databaseFile: {description: "TALON database. Created using initialize_talon_database.py.", category: "required"}
genomeBuild: {description: "Genome build (i.e. hg38) to use.", category: "required"}
minimumCoverage: {description: "Minimum alignment coverage in order to use a SAM entry.", category: "common"}
minimumIdentity: {description: "Minimum alignment identity in order to use a SAM entry.", category: "common" }
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputUpdatedDatabase: {description: "Updated TALON database."}
outputLog: {description: "Log file from TALON run."}
outputAnnot: {description: "Read annotation file from TALON run."}
outputConfigFile: {description: "The TALON configuration file."}
}
}
transcriptclean.wdl
+ 45
− 112
View file @ 589712ab
......@@ -27,7 +27,6 @@ task GetSJsFromGtf {
String outputPrefix
Int minIntronSize = 21
Int cores = 1
String memory = "8G"
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
......@@ -47,32 +46,21 @@ task GetSJsFromGtf {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
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"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
outputSJsFile: {
description: "Extracted splice junctions.",
category: "required"
}
# 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"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputSJsFile: {description: "Extracted splice junctions."}
}
}
......@@ -81,7 +69,6 @@ task GetTranscriptCleanStats {
File transcriptCleanSAMfile
String outputPrefix
Int cores = 1
String memory = "4G"
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
}
......@@ -99,24 +86,20 @@ task GetTranscriptCleanStats {
}
runtime {
cpu: cores
memory: memory
docker: dockerImage
}
parameter_meta {
transcriptCleanSAMfile: {
description: "Output SAM file from TranscriptClean",
category: "required"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
outputStatsFile: {
description: "Summary stats from TranscriptClean run.",
category: "required"
}
# inputs
transcriptCleanSAMfile: {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"}
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
outputStatsFile: {description: "Summary stats from TranscriptClean run."}
}
}
......@@ -180,81 +163,31 @@ task TranscriptClean {
}
parameter_meta {
SAMfile: {
description: "Input SAM file containing transcripts to correct.",
category: "required"
}
referenceGenome: {
description: "Reference genome fasta file.",
category: "required"
}
maxLenIndel: {
description: "Maximum size indel to correct.",
category: "advanced"
}
maxSJoffset: {
description: "Maximum distance from annotated splice junction to correct.",
category: "advanced"
}
outputPrefix: {
description: "Output directory path + output file prefix.",
category: "required"
}
correctMismatches: {
description: "Set this to make TranscriptClean correct mismatches.",
category: "common"
}
correctIndels: {
description: "Set this to make TranscriptClean correct indels.",
category: "common"
}
correctSJs: {
description: "Set this to make TranscriptClean correct splice junctions.",
category: "common"
}
dryRun: {
description: "TranscriptClean will read in the data but don't do any correction.",
category: "advanced"
}
primaryOnly: {
description: "Only output primary mappings of transcripts.",
category: "advanced"
}
canonOnly: {
description: "Only output canonical transcripts and transcript containing annotated noncanonical junctions.",
category: "advanced"
}
bufferSize: {
description: "Number of lines to output to file at once by each thread during run.",
category: "common"
}
deleteTmp: {
description: "The temporary directory generated by TranscriptClean will be removed.",
category: "common"
}
spliceJunctionAnnotation: {
description: "Splice junction file.",
category: "common"
}
variantFile: {
description: "VCF formatted file of variants.",
category: "common"
}
outputTranscriptCleanFasta: {
description: "Fasta file containing corrected reads.",
category: "required"
}
outputTranscriptCleanLog: {
description: "Log file of TranscriptClean run.",
category: "required"
}
outputTranscriptCleanSAM: {
description: "SAM file containing corrected aligned reads.",
category: "required"
}
outputTranscriptCleanTElog: {
description: "TE log file of TranscriptClean run.",
category: "required"
}
# inputs
SAMfile: {description: "Input SAM file containing transcripts to correct.", category: "required"}
referenceGenome: {description: "Reference genome fasta file.", category: "required"}
maxLenIndel: {description: "Maximum size indel to correct.", category: "advanced"}
maxSJoffset: {description: "Maximum distance from annotated splice junction to correct.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
correctMismatches: {description: "Set this to make TranscriptClean correct mismatches.", category: "common"}
correctIndels: {description: "Set this to make TranscriptClean correct indels.", category: "common"}
correctSJs: {description: "Set this to make TranscriptClean correct splice junctions.", category: "common"}
dryRun: {description: "TranscriptClean will read in the data but don't do any correction.", category: "advanced"}
primaryOnly: {description: "Only output primary mappings of transcripts.", category: "advanced"}
canonOnly: {description: "Only output canonical transcripts and transcript containing annotated noncanonical junctions.", category: "advanced"}
bufferSize: {description: "Number of lines to output to file at once by each thread during run.", category: "common"}
deleteTmp: {description: "The temporary directory generated by TranscriptClean will be removed.", category: "common"}
spliceJunctionAnnotation: {description: "Splice junction file.", category: "common"}
variantFile: {description: "VCF formatted file of variants.", category: "common"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
# outputs
outputTranscriptCleanFasta: {description: "Fasta file containing corrected reads."}
outputTranscriptCleanLog: {description: "Log file of TranscriptClean run."}
outputTranscriptCleanSAM: {description: "SAM file containing corrected aligned reads."}
outputTranscriptCleanTElog: {description: "TE log file of TranscriptClean run."}
}
}
vardict.wdl
+ 30
− 0
View file @ 589712ab
......@@ -69,4 +69,34 @@ task VarDict {
memory: memory
docker: dockerImage
}
parameter_meta {
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"}
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"}
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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