CWL Workflow: pipeline-fastq2vcf.cwl

This workflow is Open Source and may be reused according to the terms of: BSD 2-clause "Simplified" License

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

Inputs

ID	Type	Title	Doc
dbsnp	File (Optional)
sample	String (Optional)
library	String (Optional)
threads	Integer (Optional)
interval	File (Optional)
platform	String (Optional)
emit_mode	String (Optional)
readgroup	String (Optional)
reference	File
chunk_size	Integer (Optional)
input_reads	File[]
output_file	String
bwa_output_bam	String
mark_secondary	Boolean (Optional)
bqsr_known_sites	File[]
dedup_output_bam	String
qcal_output_file	String
realign_output_bam	String
realign_known_sites	File[]
qcal_plot_output_file	String (Optional)
dedup_metrics_output_file	String
qcal_plot_output_csv_file	String (Optional)

ID	Runs	Doc
hc	../algo/hc.cwl (CommandLineTool)
bwa	../algo/bwa-mem-sort.cwl (CommandLineTool)
bqsr	../stage/bqsr-flow.cwl (Workflow)	Run BQSR pre+post+plot flow
dedup	../stage/dedup-2-pass.cwl (Workflow)	run 2-pass dedup: algo LocusCollector + algo Dedup sequentially
realign	../algo/realign.cwl (CommandLineTool)

ID	Type	Label	Doc
output	File
bwa_output	File
qcal_output	File
dedup_output	File
realign_output	File
qcal_plot_output	File (Optional)
dedup_metrics_output	File (Optional)
qcal_plot_csv_output	File (Optional)