oicr-gsi / consensusCruncherWorkflow

A workflow which combines consensus cruncher and mutect2

consensusCruncher

Workflow to run extract UMIs from fastq and generate consensus Bams as well as run it thru mutect2 task and combinevariants task

Overview

Dependencies

• hg19-bwa-index 0.7.12
• samtools 1.9
• python 3.6
• picard 2.21.2
• rstats 3.6
• consensuscruncer-5.0

Usage

Cromwell

java -jar cromwell.jar run consensusCruncherWorkflow.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
outputFileNamePrefix	String	Prefix to use for output file
intervalFile	String	interval file to subset variant calls
inputRefDict	String	reference dictionary
inputRefFai	String	reference dictionary index
inputRefFasta	String	reference fasta file
inputMutectModules	String	module for mutect
inputIntervalsToParalellizeBy	String	intervals for parallelization
inputHSMetricsModules	String	module for HSmetrics
combineVariants.workflows	Array[String]	array of ids of producer workflows
combineVariants.modules	String	modules for running preprocessing
variantEffectPredictor.vcf2maf_vcfFilter	String	Filter for the vep module that is used in vcf2maf
variantEffectPredictor.vcf2maf_vepCacheDir	String	Directory of vep cache files
variantEffectPredictor.vcf2maf_vepPath	String	Path to vep script
variantEffectPredictor.vcf2maf_ncbiBuild	String	The assembly version
variantEffectPredictor.vcf2maf_modules	String	Required environment modules
variantEffectPredictor.vep_modules	String	Required environment modules
variantEffectPredictor.vep_vepCacheDir	String	Directory of cache files
variantEffectPredictor.vep_ncbiBuild	String	The assembly version

Optional workflow parameters:

Parameter	Value	Default	Description
inputGroups	Array[InputGroup]?	None	Array of fastq files to concatenate if a top-up
sortedBam	File?	None	Bam file from bwamem
sortedBai	File?	None	Bai file from bwamem

Optional task parameters:

Parameter	Value	Default	Description
concat.threads	Int	4	Number of threads to request
concat.jobMemory	Int	16	Memory allocated for this job
concat.timeout	Int	72	Hours before task timeout
concat.modules	String	"tabix/0.2.6"	Required environment modules
align.modules	String	"consensus-cruncher/5.0 data-hg19-consensus-cruncher/1.0 hg19-bwa-index/0.7.12 samtools/1.9"	Names and versions of modules to load
align.consensusCruncherPy	String	"$CONSENSUS_CRUNCHER_ROOT/bin/ConsensusCruncher.py"	Path to consensusCruncher binary
align.bwa	String	"$BWA_ROOT/bin/bwa"	Path to bwa binary
align.bwaref	String	"$HG19_BWA_INDEX_ROOT/hg19_random.fa"	Path to bwa index
align.samtools	String	"$SAMTOOLS_ROOT/bin/samtools"	Path to samtools binary
align.blist	String	"$DATA_HG19_CONSENSUS_CRUNCHER_ROOT/IDT_duplex_sequencing_barcodes.list"	Path to blacklist for barcodes
align.threads	Int	4	Number of threads to request
align.jobMemory	Int	16	Memory allocated for this job
align.timeout	Int	72	Hours before task timeout
consensus.consensusCruncherPy	String	"$CONSENSUS_CRUNCHER_ROOT/bin/ConsensusCruncher.py"	Path to consensusCruncher binary
consensus.samtools	String	"$SAMTOOLS_ROOT/bin/samtools"	Path to samtools binary
consensus.cytoband	String	"$DATA_HG19_CONSENSUS_CRUNCHER_ROOT/hg19_cytoBand.txt"	Path to cytoband for genome
consensus.genome	String	"hg19"	Which genome version to use
consensus.ccDir	String	basePrefix + ".consensuscruncher"	Placeholder
consensus.cutoff	Float	0.7	Cutoff to use to call a consenus of reads
consensus.threads	Int	8	Number of threads to request
consensus.jobMemory	Int	32	Memory allocated for this job
consensus.timeout	Int	72	Hours before task timeout
consensus.modules	String	"consensus-cruncher/5.0 data-hg19-consensus-cruncher/1.0 hg19-bwa-index/0.7.12 samtools/1.9"	Names and versions of modules to load
mutectRunDCSSC.filter_timeout	Int	12	-
mutectRunDCSSC.filter_memory	Int	16	-
mutectRunDCSSC.filter_filterExtraArgs	String?	None	-
mutectRunDCSSC.mergeStats_timeout	Int	5	-
mutectRunDCSSC.mergeStats_memory	Int	4	-
mutectRunDCSSC.mergeStats_modules	String	"gatk/4.1.6.0"	-
mutectRunDCSSC.mergeVCFs_timeout	Int	12	Hours before task timeout
mutectRunDCSSC.mergeVCFs_memory	Int	4	Memory allocated for job
mutectRunDCSSC.runMutect2_timeout	Int	24	-
mutectRunDCSSC.runMutect2_memory	Int	32	-
mutectRunDCSSC.runMutect2_threads	Int	4	-
mutectRunDCSSC.runMutect2_mutect2ExtraArgs	String?	None	-
mutectRunDCSSC.runMutect2_mutectTag	String	"mutect2"	-
mutectRunDCSSC.splitStringToArray_modules	String	""	-
mutectRunDCSSC.splitStringToArray_timeout	Int	1	-
mutectRunDCSSC.splitStringToArray_memory	Int	1	-
mutectRunDCSSC.splitStringToArray_lineSeparator	String	","	-
mutectRunDCSSC.normalBam	File?	None	Input normal file (bam or sam).
mutectRunDCSSC.normalBai	File?	None	-
mutectRunDCSSC.pon	File?	None	-
mutectRunDCSSC.ponIdx	File?	None	-
mutectRunDCSSC.gnomad	File?	None	-
mutectRunDCSSC.gnomadIdx	File?	None	-
mutectRunSSCSSC.filter_timeout	Int	12	-
mutectRunSSCSSC.filter_memory	Int	16	-
mutectRunSSCSSC.filter_filterExtraArgs	String?	None	-
mutectRunSSCSSC.mergeStats_timeout	Int	5	-
mutectRunSSCSSC.mergeStats_memory	Int	4	-
mutectRunSSCSSC.mergeStats_modules	String	"gatk/4.1.6.0"	-
mutectRunSSCSSC.mergeVCFs_timeout	Int	12	Hours before task timeout
mutectRunSSCSSC.mergeVCFs_memory	Int	4	Memory allocated for job
mutectRunSSCSSC.runMutect2_timeout	Int	24	-
mutectRunSSCSSC.runMutect2_memory	Int	32	-
mutectRunSSCSSC.runMutect2_threads	Int	4	-
mutectRunSSCSSC.runMutect2_mutect2ExtraArgs	String?	None	-
mutectRunSSCSSC.runMutect2_mutectTag	String	"mutect2"	-
mutectRunSSCSSC.splitStringToArray_modules	String	""	-
mutectRunSSCSSC.splitStringToArray_timeout	Int	1	-
mutectRunSSCSSC.splitStringToArray_memory	Int	1	-
mutectRunSSCSSC.splitStringToArray_lineSeparator	String	","	-
mutectRunSSCSSC.normalBam	File?	None	Input normal file (bam or sam).
mutectRunSSCSSC.normalBai	File?	None	-
mutectRunSSCSSC.pon	File?	None	-
mutectRunSSCSSC.ponIdx	File?	None	-
mutectRunSSCSSC.gnomad	File?	None	-
mutectRunSSCSSC.gnomadIdx	File?	None	-
mutectRunAllUnique.filter_timeout	Int	12	-
mutectRunAllUnique.filter_memory	Int	16	-
mutectRunAllUnique.filter_filterExtraArgs	String?	None	-
mutectRunAllUnique.mergeStats_timeout	Int	5	-
mutectRunAllUnique.mergeStats_memory	Int	4	-
mutectRunAllUnique.mergeStats_modules	String	"gatk/4.1.6.0"	-
mutectRunAllUnique.mergeVCFs_timeout	Int	12	Hours before task timeout
mutectRunAllUnique.mergeVCFs_memory	Int	4	Memory allocated for job
mutectRunAllUnique.runMutect2_timeout	Int	24	-
mutectRunAllUnique.runMutect2_memory	Int	32	-
mutectRunAllUnique.runMutect2_threads	Int	4	-
mutectRunAllUnique.runMutect2_mutect2ExtraArgs	String?	None	-
mutectRunAllUnique.runMutect2_mutectTag	String	"mutect2"	-
mutectRunAllUnique.splitStringToArray_modules	String	""	-
mutectRunAllUnique.splitStringToArray_timeout	Int	1	-
mutectRunAllUnique.splitStringToArray_memory	Int	1	-
mutectRunAllUnique.splitStringToArray_lineSeparator	String	","	-
mutectRunAllUnique.normalBam	File?	None	Input normal file (bam or sam).
mutectRunAllUnique.normalBai	File?	None	-
mutectRunAllUnique.pon	File?	None	-
mutectRunAllUnique.ponIdx	File?	None	-
mutectRunAllUnique.gnomad	File?	None	-
mutectRunAllUnique.gnomadIdx	File?	None	-
hsMetricsRunDCSSC.collectHSmetrics_timeout	Int	5	Maximum amount of time (in hours) the task can run for.
hsMetricsRunDCSSC.collectHSmetrics_maxRecordsInRam	Int	250000	Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed.
hsMetricsRunDCSSC.collectHSmetrics_coverageCap	Int	500	Parameter to set a max coverage limit for Theoretical Sensitivity calculations
hsMetricsRunDCSSC.collectHSmetrics_jobMemory	Int	18	Memory allocated to job
hsMetricsRunDCSSC.collectHSmetrics_filter	String	"LENIENT"	Settings for picard filter
hsMetricsRunDCSSC.collectHSmetrics_metricTag	String	"HS"	Extension for metrics file
hsMetricsRunDCSSC.bedToBaitIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunDCSSC.bedToBaitIntervals_jobMemory	Int	16	Memory allocated to job
hsMetricsRunDCSSC.bedToTargetIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunDCSSC.bedToTargetIntervals_jobMemory	Int	16	Memory allocated to job
hsMetricsRunSSCSSC.collectHSmetrics_timeout	Int	5	Maximum amount of time (in hours) the task can run for.
hsMetricsRunSSCSSC.collectHSmetrics_maxRecordsInRam	Int	250000	Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed.
hsMetricsRunSSCSSC.collectHSmetrics_coverageCap	Int	500	Parameter to set a max coverage limit for Theoretical Sensitivity calculations
hsMetricsRunSSCSSC.collectHSmetrics_jobMemory	Int	18	Memory allocated to job
hsMetricsRunSSCSSC.collectHSmetrics_filter	String	"LENIENT"	Settings for picard filter
hsMetricsRunSSCSSC.collectHSmetrics_metricTag	String	"HS"	Extension for metrics file
hsMetricsRunSSCSSC.bedToBaitIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunSSCSSC.bedToBaitIntervals_jobMemory	Int	16	Memory allocated to job
hsMetricsRunSSCSSC.bedToTargetIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunSSCSSC.bedToTargetIntervals_jobMemory	Int	16	Memory allocated to job
hsMetricsRunAllUnique.collectHSmetrics_timeout	Int	5	Maximum amount of time (in hours) the task can run for.
hsMetricsRunAllUnique.collectHSmetrics_maxRecordsInRam	Int	250000	Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed.
hsMetricsRunAllUnique.collectHSmetrics_coverageCap	Int	500	Parameter to set a max coverage limit for Theoretical Sensitivity calculations
hsMetricsRunAllUnique.collectHSmetrics_jobMemory	Int	18	Memory allocated to job
hsMetricsRunAllUnique.collectHSmetrics_filter	String	"LENIENT"	Settings for picard filter
hsMetricsRunAllUnique.collectHSmetrics_metricTag	String	"HS"	Extension for metrics file
hsMetricsRunAllUnique.bedToBaitIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunAllUnique.bedToBaitIntervals_jobMemory	Int	16	Memory allocated to job
hsMetricsRunAllUnique.bedToTargetIntervals_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
hsMetricsRunAllUnique.bedToTargetIntervals_jobMemory	Int	16	Memory allocated to job
combineVariants.jobMemory	Int	24	memory allocated to preprocessing, in GB
combineVariants.timeout	Int	20	timeout in hours
combineVariants.threads	Int	8	number of cpu threads to be used
annotation.modules	String	"samtools/1.9 bcftools/1.9 htslib/1.9 tabix/1.9"	module for running preprocessing
annotation.jobMemory	Int	24	memory allocated to preprocessing, in GB
annotation.timeout	Int	20	timeout in hours
annotation.threads	Int	8	number of cpu threads to be used
variantEffectPredictor.mergeVcfs_timeout	Int	24	Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.mergeVcfs_threads	Int	4	Requested CPU threads.
variantEffectPredictor.mergeVcfs_overhead	Int	6	Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
variantEffectPredictor.mergeVcfs_jobMemory	Int	24	Memory allocated to job (in GB).
variantEffectPredictor.mergeVcfs_extraArgs	String?	None	Additional arguments to be passed directly to the command.
variantEffectPredictor.mergeVcfs_modules	String	"gatk/4.1.7.0"	Required environment modules.
variantEffectPredictor.mergeMafs_timeout	Int	24	Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.mergeMafs_threads	Int	4	Requested CPU threads.
variantEffectPredictor.mergeMafs_jobMemory	Int	24	Memory allocated to job (in GB).
variantEffectPredictor.mergeMafs_modules	String	"tabix/0.2.6"	Required environment modules
variantEffectPredictor.vcf2maf_timeout	Int	48	Hours before task timeout
variantEffectPredictor.vcf2maf_threads	Int	4	Requested CPU threads
variantEffectPredictor.vcf2maf_jobMemory	Int	32	Memory allocated for this job (GB)
variantEffectPredictor.vcf2maf_bufferSize	Int	200	The buffer size
variantEffectPredictor.vcf2maf_minHomVaf	Float	0.7	The minimum vaf for homozygous calls
variantEffectPredictor.vcf2maf_maxfilterAC	Int	10	The maximum AC filter
variantEffectPredictor.vcf2maf_species	String	"homo_sapiens"	Species name
variantEffectPredictor.vcf2maf_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
variantEffectPredictor.tumorOnlyAlign_timeout	Int	6	Hours before task timeout
variantEffectPredictor.tumorOnlyAlign_threads	Int	4	Requested CPU threads
variantEffectPredictor.tumorOnlyAlign_jobMemory	Int	32	Memory allocated for this job (GB)
variantEffectPredictor.tumorOnlyAlign_modules	String	"bcftools/1.9 tabix/0.2.6"	Required environment modules
variantEffectPredictor.tumorOnlyAlign_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
variantEffectPredictor.vep_timeout	Int	16	Hours before task timeout
variantEffectPredictor.vep_threads	Int	4	Requested CPU threads
variantEffectPredictor.vep_jobMemory	Int	32	Memory allocated for this job (GB)
variantEffectPredictor.vep_species	String	"homo_sapiens"	Species name
variantEffectPredictor.vep_addParam	String?	None	Additional vep parameters
variantEffectPredictor.vep_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
variantEffectPredictor.subsetVcf_timeout	Int	6	Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.subsetVcf_threads	Int	4	Requested CPU threads.
variantEffectPredictor.subsetVcf_jobMemory	Int	32	Memory allocated to job (in GB).
variantEffectPredictor.subsetVcf_modules	String	"bcftools/1.9"	Required environment modules
variantEffectPredictor.subsetVcf_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
variantEffectPredictor.chromosomeArray_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.chromosomeArray_threads	Int	4	Requested CPU threads.
variantEffectPredictor.chromosomeArray_jobMemory	Int	1	Memory allocated to job (in GB).
variantEffectPredictor.getSampleNames_timeout	Int	6	Hours before task timeout
variantEffectPredictor.getSampleNames_threads	Int	4	Requested CPU threads
variantEffectPredictor.getSampleNames_jobMemory	Int	32	Memory allocated for this job (GB)
variantEffectPredictor.getSampleNames_modules	String	"vcftools/0.1.16"	Required environment modules
variantEffectPredictor.getSampleNames_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
variantEffectPredictor.targetBedTask_timeout	Int	6	Hours before task timeout
variantEffectPredictor.targetBedTask_threads	Int	4	Requested CPU threads
variantEffectPredictor.targetBedTask_jobMemory	Int	32	Memory allocated for this job (GB)
variantEffectPredictor.targetBedTask_modules	String	"bedtools/2.27 tabix/0.2.6"	Required environment modules
variantEffectPredictor.targetBedTask_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name

Outputs

Output	Type	Description