Workflow: pipeline-fastq2vcf-parallel-bwa.cwl

Fetched 2021-09-21 23:27:52 GMT

DNAseq pipeline from fastq to vcf

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Inputs

ID Type Title Doc
dedup_metrics_output_file String
chunk_size Integer (Optional)
threads Integer (Optional)
output_file String
sample String[]
platform String (Optional)
mark_secondary Boolean (Optional)
dedup_output_bam String
reference File
input_reads 2b1136880d53d31101fff40788940685[]
library String (Optional)
realign_output_bam String
realign_known_sites File[]
bwa_output_bam String
qcal_output_file String
dbsnp File (Optional)
interval File (Optional)
readgroup String[]
bqsr_known_sites File[]

Steps

ID Runs Label Doc
bam_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

bqsr

Run BQSR pre+post+plot flow

hc
../algo/hc.cwl (CommandLineTool)
realign
../algo/realign.cwl (CommandLineTool)
bwa
../algo/bwa-mem-sort.cwl (CommandLineTool)
dedup

run 2-pass dedup: algo LocusCollector + algo Dedup sequentially

Outputs

ID Type Label Doc
output File
realign_output File
qcal_output File
qcal_plot_output File (Optional)
qcal_plot_csv_output File (Optional)
dedup_output File
bwa_output File
dedup_metrics_output File (Optional)
Permalink: https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/pipeline/pipeline-fastq2vcf-parallel-bwa.cwl