Added the wdl and input json files
This commit is contained in:
Bhanu Gandham
GitHub
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e465476f99
Коммит
b950ebd65d
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## Copyright Broad Institute, 2019
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##
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## Workflows for processing RNA data for germline short variant discovery with GATK (v4) and related tools
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##
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## Requirements/expectations :
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## - BAM
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##
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## Output :
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## - A BAM file and its index.
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## - A VCF file and its index.
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## - A Filtered VCF file and its index.
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##
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## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
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## For program versions, see docker containers.
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##
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## LICENSING :
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## This script is released under the WDL source code license (BSD-3) (see LICENSE in
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## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
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## be subject to different licenses. Users are responsible for checking that they are
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## authorized to run all programs before running this script. Please see the docker
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## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed
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## licensing information pertaining to the included programs.
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workflow RNAseq {
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File inputBam
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String sampleName = basename(inputBam,".bam")
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File refFasta
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File refFastaIndex
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File refDict
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String? gatk4_docker_override
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String gatk4_docker = select_first([gatk4_docker_override, "broadinstitute/gatk:latest"])
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String? gatk_path_override
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String gatk_path = select_first([gatk_path_override, "/gatk/gatk"])
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String? star_docker_override
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String star_docker = select_first([star_docker_override, "quay.io/humancellatlas/secondary-analysis-star:v0.2.2-2.5.3a-40ead6e"])
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Array[File] knownVcfs
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Array[File] knownVcfsIndices
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File dbSnpVcf
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File dbSnpVcfIndex
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Int? minConfidenceForVariantCalling
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## Inputs for STAR
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Int? readLength
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File? zippedStarReferences
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File annotationsGTF
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## Optional user optimizations
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Int? haplotypeScatterCount
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Int scatterCount = select_first([haplotypeScatterCount, 6])
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Int? preemptible_tries
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Int preemptible_count = select_first([preemptible_tries, 3])
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call gtfToCallingIntervals {
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input:
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gtf = annotationsGTF,
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ref_dict = refDict,
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preemptible_count = preemptible_count,
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gatk_path = gatk_path,
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docker = gatk4_docker
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}
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call RevertSam {
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input:
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input_bam = inputBam,
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base_name = sampleName + ".reverted",
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sort_order = "queryname",
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call SamToFastq {
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input:
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unmapped_bam = RevertSam.output_bam,
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base_name = sampleName,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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if (!defined(zippedStarReferences)) {
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call StarGenerateReferences {
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input:
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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annotations_gtf = annotationsGTF,
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read_length = readLength,
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preemptible_count = preemptible_count,
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docker = star_docker
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}
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}
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File starReferences = select_first([zippedStarReferences,StarGenerateReferences.star_genome_refs_zipped,""])
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call StarAlign {
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input:
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star_genome_refs_zipped = starReferences,
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fastq1 = SamToFastq.fastq1,
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fastq2 = SamToFastq.fastq2,
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base_name = sampleName + ".star",
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read_length = readLength,
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preemptible_count = preemptible_count,
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docker = star_docker
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}
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call MergeBamAlignment {
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input:
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unaligned_bam = RevertSam.output_bam,
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star_bam = StarAlign.output_bam,
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base_name = ".merged",
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ref_fasta = refFasta,
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ref_dict = refDict,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call MarkDuplicates {
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input:
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input_bam = MergeBamAlignment.output_bam,
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base_name = sampleName + ".dedupped",
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call SplitNCigarReads {
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input:
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input_bam = MarkDuplicates.output_bam,
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input_bam_index = MarkDuplicates.output_bam_index,
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base_name = sampleName + ".split",
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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ref_dict = refDict,
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interval_list = gtfToCallingIntervals.interval_list,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call BaseRecalibrator {
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input:
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input_bam = SplitNCigarReads.output_bam,
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input_bam_index = SplitNCigarReads.output_bam_index,
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recal_output_file = sampleName + ".recal_data.csv",
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dbSNP_vcf = dbSnpVcf,
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dbSNP_vcf_index = dbSnpVcfIndex,
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known_indels_sites_VCFs = knownVcfs,
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known_indels_sites_indices = knownVcfsIndices,
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ref_dict = refDict,
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call ApplyBQSR {
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input:
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input_bam = SplitNCigarReads.output_bam,
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input_bam_index = SplitNCigarReads.output_bam_index,
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base_name = sampleName + ".aligned.duplicates_marked.recalibrated",
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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ref_dict = refDict,
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recalibration_report = BaseRecalibrator.recalibration_report,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call ScatterIntervalList {
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input:
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interval_list = gtfToCallingIntervals.interval_list,
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scatter_count = scatterCount,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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scatter (interval in ScatterIntervalList.out) {
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call HaplotypeCaller {
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input:
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input_bam = ApplyBQSR.output_bam,
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input_bam_index = ApplyBQSR.output_bam_index,
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base_name = sampleName + ".hc",
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interval_list = interval,
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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ref_dict = refDict,
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dbSNP_vcf = dbSnpVcf,
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dbSNP_vcf_index = dbSnpVcfIndex,
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stand_call_conf = minConfidenceForVariantCalling,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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File HaplotypeCallerOutputVcf = HaplotypeCaller.output_vcf
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File HaplotypeCallerOutputVcfIndex = HaplotypeCaller.output_vcf_index
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}
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call MergeVCFs {
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input:
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input_vcfs = HaplotypeCallerOutputVcf,
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input_vcfs_indexes = HaplotypeCallerOutputVcfIndex,
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output_vcf_name = sampleName + ".g.vcf.gz",
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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call VariantFiltration {
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input:
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input_vcf = MergeVCFs.output_vcf,
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input_vcf_index = MergeVCFs.output_vcf_index,
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base_name = sampleName + ".variant_filtered.vcf.gz",
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ref_fasta = refFasta,
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ref_fasta_index = refFastaIndex,
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ref_dict = refDict,
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preemptible_count = preemptible_count,
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docker = gatk4_docker,
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gatk_path = gatk_path
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}
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output {
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File recalibrated_bam = ApplyBQSR.output_bam
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File recalibrated_bam_index = ApplyBQSR.output_bam_index
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File merged_vcf = MergeVCFs.output_vcf
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File merged_vcf_index = MergeVCFs.output_vcf_index
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File variant_filtered_vcf = VariantFiltration.output_vcf
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File variant_filtered_vcf_index = VariantFiltration.output_vcf_index
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}
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}
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task gtfToCallingIntervals {
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File gtf
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File ref_dict
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String output_name = basename(gtf, ".gtf") + ".exons.interval_list"
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String docker
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String gatk_path
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Int preemptible_count
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command <<<
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Rscript --no-save -<<'RCODE'
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gtf = read.table("${gtf}", sep="\t")
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gtf = subset(gtf, V3 == "exon")
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write.table(data.frame(chrom=gtf[,'V1'], start=gtf[,'V4'], end=gtf[,'V5']), "exome.bed", quote = F, sep="\t", col.names = F, row.names = F)
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RCODE
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awk '{print $1 "\t" ($2 - 1) "\t" $3}' exome.bed > exome.fixed.bed
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${gatk_path} \
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BedToIntervalList \
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-I=exome.fixed.bed \
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-O=${output_name} \
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-SD=${ref_dict}
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>>>
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output {
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File interval_list = "${output_name}"
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}
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runtime {
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docker: docker
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preemptible: preemptible_count
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}
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}
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#NOTE: assuming aggregated bams & paired end fastqs
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task SamToFastq {
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File unmapped_bam
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String base_name
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String gatk_path
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String docker
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Int preemptible_count
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command <<<
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${gatk_path} \
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SamToFastq \
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--INPUT ${unmapped_bam} \
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--VALIDATION_STRINGENCY SILENT \
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--FASTQ ${base_name}.1.fastq.gz \
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--SECOND_END_FASTQ ${base_name}.2.fastq.gz
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>>>
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output {
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File fastq1 = "${base_name}.1.fastq.gz"
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File fastq2 = "${base_name}.2.fastq.gz"
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}
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runtime {
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docker: docker
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memory: "4 GB"
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disks: "local-disk " + sub(((size(unmapped_bam,"GB")+1)*5),"\\..*","") + " HDD"
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preemptible: preemptible_count
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}
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}
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task StarGenerateReferences {
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File ref_fasta
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File ref_fasta_index
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File annotations_gtf
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Int? read_length ## Should this be an input, or should this always be determined by reading the first line of a fastq input
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Int? num_threads
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Int threads = select_first([num_threads, 8])
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Int? additional_disk
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Int add_to_disk = select_first([additional_disk, 0])
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Int disk_size = select_first([100 + add_to_disk, 100])
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Int? mem_gb
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Int mem = select_first([100, mem_gb])
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String docker
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Int preemptible_count
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command <<<
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set -e
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mkdir STAR2_5
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STAR \
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--runMode genomeGenerate \
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--genomeDir STAR2_5 \
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--genomeFastaFiles ${ref_fasta} \
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--sjdbGTFfile ${annotations_gtf} \
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${"--sjdbOverhang "+(read_length-1)} \
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--runThreadN ${threads}
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ls STAR2_5
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tar -zcvf star-HUMAN-refs.tar.gz STAR2_5
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>>>
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output {
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Array[File] star_logs = glob("*.out")
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File star_genome_refs_zipped = "star-HUMAN-refs.tar.gz"
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}
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runtime {
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docker: docker
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disks: "local-disk " + disk_size + " HDD"
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cpu: threads
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memory: mem +" GB"
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preemptible: preemptible_count
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}
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}
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task StarAlign {
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File star_genome_refs_zipped
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File fastq1
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File fastq2
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String base_name
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Int? read_length
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Int? num_threads
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Int threads = select_first([num_threads, 8])
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Int? star_mem_max_gb
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Int star_mem = select_first([star_mem_max_gb, 45])
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#Is there an appropriate default for this?
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Int? star_limitOutSJcollapsed
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Int? additional_disk
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Int add_to_disk = select_first([additional_disk, 0])
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String docker
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Int preemptible_count
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command <<<
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set -e
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tar -xvzf ${star_genome_refs_zipped}
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STAR \
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--genomeDir STAR2_5 \
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--runThreadN ${threads} \
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--readFilesIn ${fastq1} ${fastq2} \
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--readFilesCommand "gunzip -c" \
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${"--sjdbOverhang "+(read_length-1)} \
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--outSAMtype BAM SortedByCoordinate \
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--twopassMode Basic \
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--limitBAMsortRAM ${star_mem+"000000000"} \
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--limitOutSJcollapsed ${default=1000000 star_limitOutSJcollapsed} \
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--outFileNamePrefix ${base_name}.
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>>>
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output {
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File output_bam = "${base_name}.Aligned.sortedByCoord.out.bam"
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File output_log_final = "${base_name}.Log.final.out"
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File output_log = "${base_name}.Log.out"
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File output_log_progress = "${base_name}.Log.progress.out"
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File output_SJ = "${base_name}.SJ.out.tab"
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}
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runtime {
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docker: docker
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disks: "local-disk " + sub(((size(fastq1,"GB")+size(fastq2,"GB")*10)+30+add_to_disk),"\\..*","") + " HDD"
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memory: (star_mem+1) + " GB"
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cpu: threads
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preemptible: preemptible_count
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}
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}
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task MergeBamAlignment {
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File ref_fasta
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File ref_dict
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File unaligned_bam
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File star_bam
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String base_name
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String gatk_path
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String docker
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Int preemptible_count
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#Using default for max_records_in_ram
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command <<<
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${gatk_path} \
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MergeBamAlignment \
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--REFERENCE_SEQUENCE ${ref_fasta} \
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--UNMAPPED_BAM ${unaligned_bam} \
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--ALIGNED_BAM ${star_bam} \
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--OUTPUT ${base_name}.bam \
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--INCLUDE_SECONDARY_ALIGNMENTS false \
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--PAIRED_RUN False \
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--VALIDATION_STRINGENCY SILENT
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>>>
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output {
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File output_bam="${base_name}.bam"
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}
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runtime {
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docker: docker
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disks: "local-disk " + sub(((size(unaligned_bam,"GB")+size(star_bam,"GB")+1)*5),"\\..*","") + " HDD"
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memory: "4 GB"
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preemptible: preemptible_count
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}
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}
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task MarkDuplicates {
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File input_bam
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String base_name
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String gatk_path
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||||
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String docker
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Int preemptible_count
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command <<<
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${gatk_path} \
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MarkDuplicates \
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--INPUT ${input_bam} \
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--OUTPUT ${base_name}.bam \
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--CREATE_INDEX true \
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--VALIDATION_STRINGENCY SILENT \
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--METRICS_FILE ${base_name}.metrics
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>>>
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output {
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File output_bam = "${base_name}.bam"
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File output_bam_index = "${base_name}.bai"
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File metrics_file = "${base_name}.metrics"
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}
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||||
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runtime {
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||||
disks: "local-disk " + sub(((size(input_bam,"GB")+1)*3),"\\..*","") + " HDD"
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||||
docker: docker
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||||
memory: "4 GB"
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||||
preemptible: preemptible_count
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||||
}
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||||
}
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||||
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task SplitNCigarReads {
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File input_bam
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||||
File input_bam_index
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||||
String base_name
|
||||
File interval_list
|
||||
|
||||
File ref_fasta
|
||||
File ref_fasta_index
|
||||
File ref_dict
|
||||
|
||||
String gatk_path
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
${gatk_path} \
|
||||
SplitNCigarReads \
|
||||
-R ${ref_fasta} \
|
||||
-I ${input_bam} \
|
||||
-O ${base_name}.bam
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_bam = "${base_name}.bam"
|
||||
File output_bam_index = "${base_name}.bai"
|
||||
}
|
||||
|
||||
runtime {
|
||||
disks: "local-disk " + sub(((size(input_bam,"GB")+1)*5 + size(ref_fasta,"GB")),"\\..*","") + " HDD"
|
||||
docker: docker
|
||||
memory: "4 GB"
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
task BaseRecalibrator {
|
||||
|
||||
File input_bam
|
||||
File input_bam_index
|
||||
String recal_output_file
|
||||
|
||||
File dbSNP_vcf
|
||||
File dbSNP_vcf_index
|
||||
Array[File] known_indels_sites_VCFs
|
||||
Array[File] known_indels_sites_indices
|
||||
|
||||
File ref_dict
|
||||
File ref_fasta
|
||||
File ref_fasta_index
|
||||
|
||||
String gatk_path
|
||||
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
${gatk_path} --java-options "-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal \
|
||||
-XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails \
|
||||
-Xloggc:gc_log.log -Xms4000m" \
|
||||
BaseRecalibrator \
|
||||
-R ${ref_fasta} \
|
||||
-I ${input_bam} \
|
||||
--use-original-qualities \
|
||||
-O ${recal_output_file} \
|
||||
-known-sites ${dbSNP_vcf} \
|
||||
-known-sites ${sep=" --known-sites " known_indels_sites_VCFs}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File recalibration_report = recal_output_file
|
||||
}
|
||||
|
||||
runtime {
|
||||
memory: "6 GB"
|
||||
disks: "local-disk " + sub((size(input_bam,"GB")*3)+30, "\\..*", "") + " HDD"
|
||||
docker: docker
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
task ApplyBQSR {
|
||||
|
||||
File input_bam
|
||||
File input_bam_index
|
||||
String base_name
|
||||
File recalibration_report
|
||||
|
||||
File ref_dict
|
||||
File ref_fasta
|
||||
File ref_fasta_index
|
||||
|
||||
String gatk_path
|
||||
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
${gatk_path} \
|
||||
--java-options "-XX:+PrintFlagsFinal -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps \
|
||||
-XX:+PrintGCDetails -Xloggc:gc_log.log \
|
||||
-XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xms3000m" \
|
||||
ApplyBQSR \
|
||||
--add-output-sam-program-record \
|
||||
-R ${ref_fasta} \
|
||||
-I ${input_bam} \
|
||||
--use-original-qualities \
|
||||
-O ${base_name}.bam \
|
||||
--bqsr-recal-file ${recalibration_report}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_bam = "${base_name}.bam"
|
||||
File output_bam_index = "${base_name}.bai"
|
||||
}
|
||||
|
||||
runtime {
|
||||
memory: "3500 MB"
|
||||
disks: "local-disk " + sub((size(input_bam,"GB")*4)+30, "\\..*", "") + " HDD"
|
||||
preemptible: preemptible_count
|
||||
docker: docker
|
||||
}
|
||||
}
|
||||
|
||||
task HaplotypeCaller {
|
||||
|
||||
File input_bam
|
||||
File input_bam_index
|
||||
String base_name
|
||||
|
||||
File interval_list
|
||||
|
||||
File ref_dict
|
||||
File ref_fasta
|
||||
File ref_fasta_index
|
||||
|
||||
File dbSNP_vcf
|
||||
File dbSNP_vcf_index
|
||||
|
||||
String gatk_path
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
Int? stand_call_conf
|
||||
|
||||
command <<<
|
||||
${gatk_path} --java-options "-Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
|
||||
HaplotypeCaller \
|
||||
-R ${ref_fasta} \
|
||||
-I ${input_bam} \
|
||||
-L ${interval_list} \
|
||||
-O ${base_name}.vcf.gz \
|
||||
-dont-use-soft-clipped-bases \
|
||||
--standard-min-confidence-threshold-for-calling ${default=20 stand_call_conf} \
|
||||
--dbsnp ${dbSNP_vcf}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_vcf = "${base_name}.vcf.gz"
|
||||
File output_vcf_index = "${base_name}.vcf.gz.tbi"
|
||||
}
|
||||
|
||||
runtime {
|
||||
docker: docker
|
||||
memory: "6.5 GB"
|
||||
disks: "local-disk " + sub((size(input_bam,"GB")*2)+30, "\\..*", "") + " HDD"
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
task VariantFiltration {
|
||||
|
||||
File input_vcf
|
||||
File input_vcf_index
|
||||
String base_name
|
||||
|
||||
File ref_dict
|
||||
File ref_fasta
|
||||
File ref_fasta_index
|
||||
|
||||
String gatk_path
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
${gatk_path} \
|
||||
VariantFiltration \
|
||||
--R ${ref_fasta} \
|
||||
--V ${input_vcf} \
|
||||
--window 35 \
|
||||
--cluster 3 \
|
||||
--filter-name "FS" \
|
||||
--filter "FS > 30.0" \
|
||||
--filter-name "QD" \
|
||||
--filter "QD < 2.0" \
|
||||
-O ${base_name}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_vcf = "${base_name}"
|
||||
File output_vcf_index = "${base_name}.tbi"
|
||||
}
|
||||
|
||||
runtime {
|
||||
docker: docker
|
||||
memory: "3 GB"
|
||||
disks: "local-disk " + sub((size(input_vcf,"GB")*2)+30, "\\..*", "") + " HDD"
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
task MergeVCFs {
|
||||
Array[File] input_vcfs
|
||||
Array[File] input_vcfs_indexes
|
||||
String output_vcf_name
|
||||
|
||||
Int? disk_size = 5
|
||||
|
||||
String gatk_path
|
||||
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
# Using MergeVcfs instead of GatherVcfs so we can create indices
|
||||
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
|
||||
command <<<
|
||||
${gatk_path} --java-options "-Xms2000m" \
|
||||
MergeVcfs \
|
||||
--INPUT ${sep=' --INPUT=' input_vcfs} \
|
||||
--OUTPUT ${output_vcf_name}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_vcf = output_vcf_name
|
||||
File output_vcf_index = "${output_vcf_name}.tbi"
|
||||
}
|
||||
|
||||
runtime {
|
||||
memory: "3 GB"
|
||||
disks: "local-disk " + disk_size + " HDD"
|
||||
docker: docker
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
task ScatterIntervalList {
|
||||
|
||||
File interval_list
|
||||
Int scatter_count
|
||||
String gatk_path
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
set -e
|
||||
mkdir out
|
||||
${gatk_path} --java-options "-Xms1g" \
|
||||
IntervalListTools \
|
||||
--SCATTER_COUNT=${scatter_count} \
|
||||
--SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
|
||||
--UNIQUE=true \
|
||||
--SORT=true \
|
||||
--INPUT=${interval_list} \
|
||||
--OUTPUT=out
|
||||
|
||||
python3 <<CODE
|
||||
import glob, os
|
||||
# Works around a JES limitation where multiples files with the same name overwrite each other when globbed
|
||||
intervals = sorted(glob.glob("out/*/*.interval_list"))
|
||||
for i, interval in enumerate(intervals):
|
||||
(directory, filename) = os.path.split(interval)
|
||||
newName = os.path.join(directory, str(i + 1) + filename)
|
||||
os.rename(interval, newName)
|
||||
print(len(intervals))
|
||||
f = open("interval_count.txt", "w+")
|
||||
f.write(str(len(intervals)))
|
||||
f.close()
|
||||
CODE
|
||||
>>>
|
||||
|
||||
output {
|
||||
Array[File] out = glob("out/*/*.interval_list")
|
||||
Int interval_count = read_int("interval_count.txt")
|
||||
}
|
||||
|
||||
runtime {
|
||||
disks: "local-disk 1 HDD"
|
||||
memory: "2 GB"
|
||||
docker: docker
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
task RevertSam {
|
||||
File input_bam
|
||||
String base_name
|
||||
String sort_order
|
||||
|
||||
String gatk_path
|
||||
|
||||
String docker
|
||||
Int preemptible_count
|
||||
|
||||
command <<<
|
||||
${gatk_path} \
|
||||
RevertSam \
|
||||
--INPUT ${input_bam} \
|
||||
--OUTPUT ${base_name}.bam \
|
||||
--VALIDATION_STRINGENCY SILENT \
|
||||
--ATTRIBUTE_TO_CLEAR FT \
|
||||
--ATTRIBUTE_TO_CLEAR CO \
|
||||
--SORT_ORDER ${sort_order}
|
||||
>>>
|
||||
|
||||
output {
|
||||
File output_bam = "${base_name}.bam"
|
||||
}
|
||||
|
||||
runtime {
|
||||
docker: docker
|
||||
disks: "local-disk " + sub(((size(input_bam,"GB")+1)*5),"\\..*","") + " HDD"
|
||||
memory: "4 GB"
|
||||
preemptible: preemptible_count
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
{
|
||||
"##_COMMENT1": "Input",
|
||||
"RNAseq.inputBam": "gs://gatk-test-data/rna_bam/NA12878_b37/NA12878.bam",
|
||||
|
||||
"##_COMMENT2": "REFERENCE FILES",
|
||||
"RNAseq.refFasta": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta",
|
||||
"RNAseq.refFastaIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai",
|
||||
"RNAseq.refDict": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict",
|
||||
|
||||
"##_COMMENT4": "RESOURCE FILES",
|
||||
"RNAseq.dbSnpVcf": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf",
|
||||
"RNAseq.dbSnpVcfIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf.idx",
|
||||
"RNAseq.knownVcfs": [
|
||||
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf",
|
||||
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf"
|
||||
],
|
||||
"RNAseq.knownVcfsIndices": [
|
||||
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx",
|
||||
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf.idx"
|
||||
],
|
||||
"RNAseq.annotationsGTF": "gs://gatk-test-data/intervals/star.gencode.v19.transcripts.patched_contigs.gtf",
|
||||
|
||||
"##_COMMENT4": "DOCKERS",
|
||||
"#RNAseq.gatk4_docker_override": "String? (optional)",
|
||||
"#RNAseq.star_docker_override": "String? (optional)",
|
||||
"#RNAseq.gitc_docker_override": "String? (optional)",
|
||||
|
||||
"##_COMMENT5": "PATHS",
|
||||
"#RNAseq.gatk_path_override": "/gatk/gatk",
|
||||
|
||||
"##_COMMENT6": "PREEMPTIBLES",
|
||||
"##RNAseq.preemptible_tries": "(optional) Int?",
|
||||
|
||||
"##_COMMENT7": "Misc",
|
||||
"#RNAseq.StarAlign.num_threads": "(optional) Int?",
|
||||
"#RNAseq.StarAlign.star_limitOutSJcollapsed": "(optional) Int?",
|
||||
"RNAseq.StarAlign.additional_disk": "50",
|
||||
"#RNAseq.StarAlign.star_mem_max_gb": "(optional) Int?",
|
||||
"RNAseq.StarGenerateReferences.addtional_disk": 50,
|
||||
"#RNAseq.StarGenerateReferences.num_threads": "(optional) Int?",
|
||||
"#RNAseq.StarGenerateReferences.mem_gb": "(optional) Int?",
|
||||
"#RNAseq.haplotypeScatterCount": "(optional) Int?",
|
||||
"#RNAseq.use_gatk4_for_all_tools": "(optional) Boolean",
|
||||
"#RNAseq.minConfidenceForVariantCalling": "(optional) Int?",
|
||||
"#RNAseq.zippedStarReferences": "(optional) File?",
|
||||
"#RNAseq.readLength": "(optional) Int?"
|
||||
}
|
||||
Загрузка…
Ссылка в новой задаче