WGS processing workflow for single sample - Common Workflow Language Viewer

Workflow: WGS processing workflow for single sample

Fetched 2023-01-11 20:12:33 GMT

Verified with cwltool version 3.1.20221201130942

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This workflow is Open Source and may be reused according to the terms of: GNU Affero General Public License v3.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
fastq1	File [FASTQ]	One of set of pair-end FASTQs (R1)
fastq2	File [FASTQ]	One of set of pair-end FASTQs (R2)
sample	String	Sample Name
headhtml	File [plain text format (unformatted)]	Header for HTML report
tailhtml	File [plain text format (unformatted)]	Footer for HTML report
reference	File [FASTA]	Reference genome
clinvarvcf	File [VCF]	Reference VCF for ClinVar
knownsites	File [VCF]	VCF of known polymorphic sites for BQSR
reportfunc	File	Function used to create HTML report
scattercount	String	Desired split for variant calling

Steps

ID	Runs	Label	Doc
fastqc	fastqc.cwl (CommandLineTool)	Quality check on FASTQ
samtools-sort	samtools-sort.cwl (CommandLineTool)	Sort BAM
samtools-index	samtools-index.cwl (CommandLineTool)	Index BAM
generate-report	report-wf.cwl (Workflow)	Report generation workflow
haplotypecaller	scatter-gatk-wf-with-interval.cwl (Workflow)	Scattered variant calling workflow
mark-duplicates	mark-duplicates.cwl (CommandLineTool)	Mark duplicates using GATK (Picard)
bwamem-samtools-view	bwamem-samtools-view.cwl (CommandLineTool)	Align FASTQs with BWA

Outputs

ID	Type	Label	Doc
gvcf	File [VCF]	GVCF generated from GATK Haplotype Caller
qc-zip	File[]	Zip files of FASTQ QC report and associated data
report	File [plain text format (unformatted)]	ClinVar variant report
qc-html	File[] [plain text format (unformatted)]	FASTQ QC reports

Permalink:

https://w3id.org/cwl/view/git/ef89d0aabd706c59168537f69742e570373fdd84/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl