CWL Workflow: pipeline-fastq2vcf-distr.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)
shard	String[]
sample	String (Optional)
library	String (Optional)
threads	Integer (Optional)
interval	File (Optional)
platform	String (Optional)
readgroup	String (Optional)
reference	File
chunk_size	Integer
input_reads	File[]
output_file	String
extract_chunks	String[]
mark_secondary	Boolean (Optional)
sort_reference	File (Optional)
bam_compression	Integer (Optional)
min_std_max_min	Integer[] (Optional)
sort_output_bam	String
bqsr_known_sites	File[]
dedup_output_bam	String
qcal_output_file	String
realign_output_bam	String
minimum_seed_length	Integer (Optional)
realign_known_sites	File[]
input_reads_index_file	File
dedup_metrics_output_file	String

ID	Runs	Doc
hc	../stage/hc-distr.cwl (Workflow)
bwa	../algo/bwa-mem-sort-with-fastq-slicer.cwl (CommandLineTool)
bqsr	../stage/bqsr-flow-distr.cwl (Workflow)	Run BQSR pre+post+plot flow with distribution
dedup	../stage/dedup-2-pass-distr.cwl (Workflow)	run 2-pass dedup: algo LocusCollector + algo Dedup sequentially in distributed mode
realign	../stage/realign-distr.cwl (Workflow)
sort_merge	../algo/bam-merge.cwl (CommandLineTool)	merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used

ID	Type	Label	Doc
output	File
qcal_output	File
sort_output	File
dedup_output	File
realign_output	File
qcal_plot_output	File (Optional)
dedup_metric_output	File (Optional)
qcal_plot_csv_output	File (Optional)