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AggregatedBamQC.wdl
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version 1.0
## Copyright Broad Institute, 2018
##
## This WDL pipeline implements data processing according to the GATK Best Practices (June 2016)
## for human whole-genome and exome sequencing data.
##
## Runtime parameters are often optimized for Broad's Google Cloud Platform implementation.
## For program versions, see docker containers.
##
## LICENSING :
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
## be subject to different licenses. Users are responsible for checking that they are
## authorized to run all programs before running this script. Please see the docker
## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed
## licensing information pertaining to the included programs.
import "https://raw.githubusercontent.com/trinhan/wgsAlignment/main/Qc.wdl?token=ABVSYKAUTHJEFZZC72KDE4DA6EGTI" as QC
import "https://raw.githubusercontent.com/trinhan/wgsAlignment/main/DNASeqStructs.wdl?token=ABVSYKHO756SWW4KHSKBODLA6EGWK"
# WORKFLOW DEFINITION
workflow AggregatedBamQC {
input {
File base_recalibrated_bam
File base_recalibrated_bam_index
String base_name
String sample_name
String recalibrated_bam_base_name
File haplotype_database_file
DNASeqSingleSampleReferences references
PapiSettings papi_settings
File? fingerprint_genotypes_file
File? fingerprint_genotypes_index
}
# QC the final BAM (consolidated after scattered BQSR)
call QC.CollectReadgroupBamQualityMetrics as CollectReadgroupBamQualityMetrics {
input:
input_bam = base_recalibrated_bam,
input_bam_index = base_recalibrated_bam_index,
output_bam_prefix = base_name + ".readgroup",
ref_dict = references.reference_fasta.ref_dict,
ref_fasta = references.reference_fasta.ref_fasta,
ref_fasta_index = references.reference_fasta.ref_fasta_index,
preemptible_tries = papi_settings.agg_preemptible_tries
}
# QC the final BAM some more (no such thing as too much QC)
call QC.CollectAggregationMetrics as CollectAggregationMetrics {
input:
input_bam = base_recalibrated_bam,
input_bam_index = base_recalibrated_bam_index,
output_bam_prefix = base_name,
ref_dict = references.reference_fasta.ref_dict,
ref_fasta = references.reference_fasta.ref_fasta,
ref_fasta_index = references.reference_fasta.ref_fasta_index,
preemptible_tries = papi_settings.agg_preemptible_tries
}
if (defined(haplotype_database_file) && defined(fingerprint_genotypes_file)) {
# Check the sample BAM fingerprint against the sample array
call QC.CheckFingerprint as CheckFingerprint {
input:
input_bam = base_recalibrated_bam,
input_bam_index = base_recalibrated_bam_index,
haplotype_database_file = haplotype_database_file,
genotypes = fingerprint_genotypes_file,
genotypes_index = fingerprint_genotypes_index,
output_basename = base_name,
sample = sample_name,
preemptible_tries = papi_settings.agg_preemptible_tries
}
}
# Generate a checksum per readgroup in the final BAM
call QC.CalculateReadGroupChecksum as CalculateReadGroupChecksum {
input:
input_bam = base_recalibrated_bam,
input_bam_index = base_recalibrated_bam_index,
read_group_md5_filename = recalibrated_bam_base_name + ".bam.read_group_md5",
preemptible_tries = papi_settings.agg_preemptible_tries
}
output {
File read_group_alignment_summary_metrics = CollectReadgroupBamQualityMetrics.alignment_summary_metrics
File read_group_gc_bias_detail_metrics = CollectReadgroupBamQualityMetrics.gc_bias_detail_metrics
File read_group_gc_bias_pdf = CollectReadgroupBamQualityMetrics.gc_bias_pdf
File read_group_gc_bias_summary_metrics = CollectReadgroupBamQualityMetrics.gc_bias_summary_metrics
File calculate_read_group_checksum_md5 = CalculateReadGroupChecksum.md5_file
File agg_alignment_summary_metrics = CollectAggregationMetrics.alignment_summary_metrics
File agg_bait_bias_detail_metrics = CollectAggregationMetrics.bait_bias_detail_metrics
File agg_bait_bias_summary_metrics = CollectAggregationMetrics.bait_bias_summary_metrics
File agg_gc_bias_detail_metrics = CollectAggregationMetrics.gc_bias_detail_metrics
File agg_gc_bias_pdf = CollectAggregationMetrics.gc_bias_pdf
File agg_gc_bias_summary_metrics = CollectAggregationMetrics.gc_bias_summary_metrics
File agg_insert_size_histogram_pdf = CollectAggregationMetrics.insert_size_histogram_pdf
File agg_insert_size_metrics = CollectAggregationMetrics.insert_size_metrics
File agg_pre_adapter_detail_metrics = CollectAggregationMetrics.pre_adapter_detail_metrics
File agg_pre_adapter_summary_metrics = CollectAggregationMetrics.pre_adapter_summary_metrics
File agg_quality_distribution_pdf = CollectAggregationMetrics.quality_distribution_pdf
File agg_quality_distribution_metrics = CollectAggregationMetrics.quality_distribution_metrics
File agg_error_summary_metrics = CollectAggregationMetrics.error_summary_metrics
File? fingerprint_summary_metrics = CheckFingerprint.summary_metrics
File? fingerprint_detail_metrics = CheckFingerprint.detail_metrics
}
meta {
allowNestedInputs: true
}
}