bwa_gatk
WDL workflow to align sequencing data using BWA and perform QC steps with GATK
WDL Version
1.0
Nested Inputs Not Allowed
RUN WITH
sprocket run --entrypoint bwa_gatk ww-bwa-gatk.wdlww-bwa-gatk.wdl [INPUTS]...
authorEmma Bishopemailebishop@fredhutch.orgurlhttps://raw.githubusercontent.com/getwilds/wilds-wdl-library/refs/heads/main/pipelines/ww-bwa-gatk/ww-bwa-gatk.wdlInputs
Required Inputs
Name
Type
Description
reference_fastaFileReference genome FASTA file
Reference genome FASTA file
reference_fasta_indexFileIndex for reference genome FASTA file
Index for reference genome FASTA file
dbsnp_vcfFiledbSNP VCF file for known variant sites
dbSNP VCF file for known variant sites
known_indels_vcfArray[File]Array of VCF files with known indel sites
Array of VCF files with known indel sites
samplesArray[BwaSample]List of BwaSample objects, each containing the sample name, forward reads FASTQ, and optionally reverse reads FASTQs
List of BwaSample objects, each containing the sample name, forward reads FASTQ, and optionally reverse reads FASTQs
Other Inputs
Name
Type
Default
Description
cpu_coresInt4Number of CPUs to use for BWA alignment and GATK processing
Number of CPUs to use for BWA alignment and GATK processing
memory_gbInt8Memory allocation in GB
Memory allocation in GB
Outputs
Name
Type
Expression
Description
duplicate_metricsArray[File]mark_duplicates.duplicate_metricsArray of duplicate marking statistics for each sample
Array of duplicate marking statistics for each sample
recalibrated_bamArray[File]base_recalibrator.recalibrated_bamArray of BAM files with recalibrated base quality scores
Array of BAM files with recalibrated base quality scores
recalibrated_baiArray[File]base_recalibrator.recalibrated_baiArray of corresponding index files for each recalibrated bam file
Array of corresponding index files for each recalibrated bam file
recalibration_reportArray[File]base_recalibrator.recalibration_reportArray of base recalibration report tables
Array of base recalibration report tables